After East Timor's independence was approved, pro-Jakarta militias ran amok and killed, burned and looted everything they could for a two week period as an act of revenge to get even with those who supported independence. The militias were armed with machetes, daggers, spears and homemade guns. Around 1,500 people were killed; an untold number of women were raped; 300,000 were made homeless; 80 percent of the buildings were destroyed, and three quarters of the population fled their homes, with 250,000 fleeing to West Timor. Property destruction was on an almost inconceivable scale, apparently aimed at "the virtual demolition of the physical basis for survival in the territory," according to Noam Chomsky. reported: “On August 31, 1999, East Timorese went to the polls to vote for autonomy within Indonesia or fully-fledged independence. But as noted, despite clear signals that the Indonesian military and its Timorese militia allies would respond with violence to a vote for full independence, the U.N. assigned responsibility for "security" to the Indonesian armed forces. When widespread violence and destruction broke out on September 2, the U.N. and the international community were therefore unable (and initially unwilling) to address the consequences of the plebiscite that they themselves had overseen. When the results of the plebiscite were made public, the Indonesian military and its allies implemented a well-prepared and systematic policy of murder and destruction ("Operation Global Clean-Sweep") aimed at preserving Indonesian control over the territory, or at least a substantial portion of it. [Source:]

Andrea K. Molnar of Northern Illinois University wrote: “ Even before the votes were counted the militia began the promised blood bath aiming at known and suspected independence sympathizers. The violence was not only aimed at the general population but also at international journalists, observers, and UNAMET staff members. UNAMET staff from the districts had to withdraw to Dili in midst of the violence and one of the first UNAMET offices to be evacuate was that from Bobonaro district. Many East Timorese (over 250,000 people), against their will, were herded by the militia on to large construction trucks and any other available vehicle and forcefully evacuated to west Timor, to the Atambua region. The Indonesian military and police also aided in such forced evacuations. In Indonesian Timor these ‘refugees’ ended up living in overpopulated, disease filled, malnourished and militia controlled refugee camps. [Source: Andrea K. Molnar, Northern Illinois University, Department of Anthropology and Center for Southeast Asian Studies, May 2005 ,]

The attacks were often carefully planned. They were carried out by around 30,000 members of 14 militia organizations in East Timor. The members used sophisticated weapons which hinted that the whole thing was orchestrated by the Indonesian government and military. In some cases the militias were financed, directed and even armed by the Indonesian military.

The 10,000 or so Indonesian troops and police in East Timor did little to stop the violence and in some cases joined in. One Western diplomat told the Washington Post, "The militias and military together are just burning and looting. There's no more distinction between the two.” The violence ended on September 7 when Indonesia declared martial law.

Why all violence after the referendum rather before it? A western diplomat told the Washington Post, the goal appeared to be "to destroy everything, leave you guys with nothing, and then give you your independence...It's Stalinist. Its like what I read about Stalin in the 1930s, ripping up places like Central Asia and deporting people." Graffiti left in Dili read “A Free East Timor Will Eat Stones” Maybe, the Indonesian military was trying to send a message to separatists in Aceh, Irian Jaya and elsewhere, saying this is what will happen to you if you try to secede.

Details of the atrocities committed by the militias and Indonesian military personnel against the East Timorese people have been documented by a number of sources, such as Cristalis 2002, Hainsworth and McCloskey 2000, Kingsbury 2000, Martin 2001, Fox and Soares 2000, Savage 2002 among others.

Pro-Indonesia Militias in East Timor

The pro-Indonesia side was represented by militias with names like Aitarak ("Thorn"), Mahidi ("Live or Die with Indonesia") and Besi Merah Putih ("Red and White Irons", a reference to the colors on the Indonesian flag). The militias were often little more than gangs made up of unemployed laborers or school drop outs. Launching raids from bases in West Timor, they torched homes and terrorized, killed, tortured and raped people suspected of supporting Fretilin guerillas and the pro-independence drive.

Describing the militias Sidney Jones of Human Rights Watch wrote in the New York Times, "These are not community-based self-defense forces, despite the claims of some militia leaders. They are a shadow force of the Indonesian military, with whom militia leaders have long-established ties." Some militia members said they only took part because they were manipulated by militia leaders and feed amphetamines to make them agitated and more likely to commit violence. One militia member told the New York Times, "We were forced to join the militia. If we had a choice who would want to be in the militia? But if I'd refused they would have killed me.”

Many of the militias were assembled by the Indonesian military in the beginning of 1999 in what appears to have been a thought-out plan to disrupt the August referendum and terrorize supporters of independence. One militia member told the Los Angeles Times, “When [the Indonesian military] came to them they said, ‘You’re a friend so make a [militia]. If you are not our friend then you are enemy.’” Another said he saw farmers given guns by the Indonesian military and were promised $2.50 and a bag of rice for every person he killed.

Andrea K. Molnar of Northern Illinois University wrote: “ Between October 1998 and January 1999 the Indonesian military operations reorganized the already existing paramilitary groups (militia). These Indonesian army trained and supported militias became active in discouraging pro-independence East Timorese from even considering separation form the Indonesian state through a program of terror. As Soares (2000:65-68) explains, “Tim Alfa in Los Palos and Saka and Makikit in Baucau became ‘Civil Defense Units’ (Keamanan Rakyat: KAMRA).” These militias were located in the eastern part of East Timor. The military also set up militia groups in central and western East Timor, namely, the Mahidi (Dead or Alive for Integration) and Halilintar (Lighting) in the Maliana region (ibid). [Source: Andrea K. Molnar, Northern Illinois University, Department of Anthropology and Center for Southeast Asian Studies, May 2005 ,]

“This program of terror only intensified throughout 1999; before and during the arrival of the United Nations Assistance Mission to East Timor (UNAMET) (Kingsbury 2000:27). New militia groups were created by the military. The following militia groups were came into existence (Soares 2000:67): Sera (Sera Malik); Hametin in the Bobonaro district; Dadurus Merah Putih, ABLAI (struggle for Integration) in Same, Manufahi district; Laksaur (eagle) led by Olivio ‘Moruk’ Mendonça; Besi Merah Putih (Red and White Iron) led by Manuel de Sousa in Liquiça district; Darah Merah (Red Blood) led by Lafaher Saburai in the Ermera district; Naga Merah (Red Dragon) in the Ermera district; and Aitarak (Thorn) led by Erico Guterres in Dili; Rajawali; Jati Merah Putih (Real Red and While) in the Los Palos district; Mahadomi in the Manatuto district led by Aquino Caldas and vital Doutel Sarmento; Pana in the Liquiça district; and Sakunar in the Oecussi district led by Simão Lopes.

Rape and Pillaging by the Militias After the 1999 East Timor Referendum

In the rampage after the independence referendum, militias fired into the international Red Cross compound, shot at the Australia ambassador’s car and attacked the home of Nobel Peace Prize winner Carlos Belo. The courthouse in Dili was looted and trashed: windows were broken; computers and judges robes were stolen; files were taken and the furniture was tossed around.

The population of Dili dropped from 175,000 to 70,000. Most of those who remained lived in tents on the beach and parks. Smoke filled the air, streets were abandoned and vehicles were gutted. About to 95 percent of the towns Maliana, Balibo, Glenois and Suai were destroyed. Journalist, aid workers and election observers were all intimidated into fleeing the country by militias shouting "Kill them! Kill them! Kill the Australian journalists!." Only a handful remained, holed up in the United Nations compound.

The governor's mansion was looted and documents were scattered all over the place. Several banks, two radio stations, the Voice of East Timor newspaper, the Mahkota Hotel, other hotels, the Catholic diocese office and most of the shops and restaurants in the Central business district of Dili were looted and burned. One of the cities two hospitals was destroyed. The other managed to stay open. reported: A number of younger Timorese women are reported to have been killed as known or suspected independence supporters. Reports also reached the international media of young Timorese women being raped, or abducted for use as sex-slaves. A representative of the aid agency World Vision stated in mid-October that "Apparently when the militias went on their rampage, they herded people into the marketplace to make forced evacuations and during that time, many young girls were dragged away and raped by the pro-integrationist forces." (ABC [Australia] News Online, October 20, 1999.) Some of the worst cases of sexual assault, accompanied by mass killing, occurred at Suai on September 6 (see below). Rape was also allegedly widespread in the detention camps in West Timor, according to the United Nations Special Rapporteur on Violence against Women, Radhika Coomaraswamy, who was sent to Dili. [Source:]

Accounts of Destruction By the Militias After the 1999 East Timor Referendum

One of those who remained, Dutch journalist Tjiske Lingsma told the New York Times by phone. "All day around Dili buildings have been set in fire. Just after dark we saw two huge fires not far from the United Nations compound. The whole city is being destroyed and houses are being looted. the situation is getting worse and worse." East Timorese pursued by the machete-wielding militias trying get inside the United Nations compound threw cut themselves at locked gates and tossed babies over the razor wire fences. One man told Newsweek that he was targeted by the militias for talking with independence activists. He was told to dig his own grave and was dressed in a white shroud. Militia members buried him up to his neck and forced him to read a Muslim prayer.

A woman who had remained in her house until the militias arrived, later told the New York Times, "I head the leader shouting, 'Burn that house, burn that house.' 'This house' meant our house. They came on motorcycles, hitting at things with rifle butts and sticks, hitting houses and fences, breaking windows, shooting their guns." She fled to a grove of mango trees and watched as her house was burnt down.

On September 4, Matt Frei of BBC Online provided eyewitness testimony of the murder of a young Timorese independence supporter. "While I was running towards the UN compound a pro-independence supporter was being hunted down like an animal. The young man fell after being hit on the head with a machete. Then six black T-shirts descended on him. A colleague hiding in a shack just opposite the gates to the UN compound filmed the whole thing. It took only 30 seconds to hack the man to pieces. The attack was so ferocious that bits of him were literally flying off. The sound reminded me of a butchers' shop — the thud of cleaved meat, I'll never forget it." (Frei, BBC Online, September 4, 1999.) Also on September 4, Joao Brito, a young Timorese man, claimed to have witnessed the killing of possibly hundreds of people in the town of Ermera. Indonesian soldiers "called house-to-house and they burned out the political leaders," he said later. "When the houses burnt, they let the women and children out, but they pushed the men back into the fire where they died." (Dennis Schulz, The Age, September 16, 1999.) [Source:]

Victims of Violence After the 1999 East Timor Referendum

Many of the victims of violence after the 1999 East Timor Referendum were people who were believed to be supporters of the separatist guerrillas. One man, whose family was desperately hungry, drove his car towards Dili to get his food. Militia members stopped his car and told him to get out. He was shot on the spot. Describing the death of his brother, one man told the New York Times, "They started to beat Afonso with their rifle butts. He put his hands over his head and started to scream. Then they shot Afonso between the legs, and he fell on his face. He crawled on the ground to a tree, and he lay on his back at the foot of the tree, looking at the sky." He lifts his head and repeated the same phrase twice before he died: "Look after my mother. Look after my mother."

U.N. observer Pamela Sexton told Reuters and Newsweek, "The man we encountered was sliced numerous times on either arm and his stomach. He was literally covered with blood but was walking...I think maybe his intestines were out... I was asked to help out because I have some training in first aid. Where do you put a tourniquet on someone who has been sliced all over their body—cuts to the bone?" "We wrapped him up and put him in the car, but the wrapping didn't do much because within minutes the whole white sheet was covered in blood." Sexton drove the man to a clinic where he died hours later. The next day the clinic was burned down.

Mass graves were discovered. One well discovered by Australia peacekeepers had 30 bodies in it, several of them headless. Nearby they found meat hooks with blood encrusted on them. It is believed that victims were tortured and then hung like slabs of meat before they were thrown to their deaths.

Timorese leader José Ramos-Horta spoke of "information that many males have been disposed of, have been killed and dumped into the sea." ( Stephen Powell, Reuters, September 7, 1999.) The Guardian's John Aglionby wrote: "Villagers [who told] of men being marched to the waterfront in Dili and gunned down out of view of observers trapped inside safe houses." (The Guardian, September 9, 1999.) The following day, Aglionby described "a young man [who] ran into the house telling a terrible story. He had come from the port, where he and some pro-independence friends had been trying to leave on a ship. The women boarded, but the men were dragged away. Five were stabbed to death in front of him and their bodies dumped in the sea." (The Guardian, September 10, 1999.) [Source: |+|]

Craig Skehan and Malcolm Brown of The Sydney Morning Herald reported that One distraught young mother said she witnessed the murder of two refugees on the back of a truck inside West Timor. She said she saw the two men tied up in a truck by militiamen on a road inside West Timor. "Suddenly, in front of lots of people, a militia member drew a sword and slowly stabbed one of the people in the truck. Lots of blood began gushing, flooding the floor of the truck until it began to drip out," she said. "The other man's hands and feet were tied like a pig and he was thrown like a bag of rice onto the asphalt then thrown into another truck." Another man said he watched terrified at the West Timor port of Akapupu, near Atumbua at the northern end of the border, as militia used machetes to kill men alleged to be independence supporters. They were among East Timorese disembarking from a ship which had come from Dili. "Other men had their hands tied and they were put on trucks and taken away," said one source, who is collecting accounts for presentation to the international community. [Source: Skehan and Brown, Sydney Morning Herald, September 10, 1999]

Agence France-Presse cited "reports [that] men in UN gear were loading young men into C-130 aircraft for unknown destinations." (AFP, September 13, 1999.) In an "urgent action" of September 14, the East Timor Human Rights Centre in Australia reported that "Indonesian military, police and militia are patrolling both Kupang and Atambua [in West Timor], and are carrying out operations, particularly at night, where they search for East Timorese men, including independence supporters. Between Monday September 6 and Thursday September 9, the streets were deserted, and the town extremely tense. Sources fear that East Timorese men and independence supporters are being rounded up to be assassinated."

Attacks on Priests, Nuns and Churches in the Violence After the 1999 Referendum

Priests and nuns were among the first to be targeted and killed by the militias in the violence in East Timor that followed the 1999 Independence referendum. Four priests were among the 100 or so people killed in a particularly brutal attack on a church in the southern town of Suai. Rev. Francisco Barreto, head of the Catholic aid agency Caritas, was killed. Both of East Timor's bishops were forced to flee. A vehicle carrying three priest and one nun was ambushed and the occupants were killed with by bullets or machetes.

The Catholic Church attempted to reconcile the two opposing parties despite of the continued violence. On 29 August, in Suai, Cova Lima district, Bishop Belo and Father Hilario Madeira, brokered a peace settlement and mass between the pro independence group, represented by the CNRT and the Mahadi militia that were representing the pro-Indonesia group (Soares 2000:75). However, other militia members were not in agreement and this peace agreement sanctioned by the Church was ignored.[Source: Andrea K. Molnar, Northern Illinois University, Department of Anthropology and Center for Southeast Asian Studies, May 2005 ,]

One nun later told the Washington Post, "It was really frightening. We couldn't go out of the house. We could see a lot of fires. It looked like they would use diesel gas, because the fires would be big black balls, and then you could see white smoke from houses. That was everywhere." "It was remarkable. There was shooting going on, and people were running for their lives. But others were looting the stores, very calmly, as though they were so relaxed." She said she saw some of the goods loaded onto military trucks.

Describing what a told him about the attack on the church that left 27 dead in Suai, Doug Struck wrote in the Washington Post, "The militiamen had lined up outside the old wooden church filled with refugees...and a young Indonesian priest stepped out dressed in his clerical robes to meet the trouble...A burst of gunfire cut him down. The Reverend Francisco followed. The blood soaked his white robes."

The militiamen waited for the senior parish priest, the Reverend Hialrio. When he did not emerge, they kicked down the door to his study and sprayed him with automatic fire...The militiamen entered the church filled with refugees, and began firing long bursts from their weapons. Then they threw hand grenades into the huddled victims. One, two, three grenades. As they left, blood flowed down the doorstep." Most of the victims were women, children and elderly men. Younger men had left days earlier. The nun said, People went to the church because that's where they felt safe. They felt being near the priest was protection.

Michael Valpy wrote in The Globe and Mail: “The number of victims and their identities are uncertain. What is known is that most were women and girls. The evidence attests to that: the jumble of bras, underpants and sanitary napkins on the steps leading up to the church; the children's leg bones; a hank of a woman's hair; the scorched skeletal remains of two women behind the church; the thick bloodstain on a schoolroom door, covered by bougainvillea petals baking beneath the sun. ... What happened was male savagery as old as history — rape, killing, burning, razing — in a church, a school, in the adjacent huge, grey, concrete shell of a cathedral called Ave Maria under construction to the glory of God. Savagery against the defenceless, as women and children usually are; vengeance on a people who voted for independence from their Indonesian military overlords and landowners." Afterwards, surviving "women and children were carted away on trucks to Indonesia's neighbouring West Timor province, about 30 kilometres away, where they are still being held. The whereabouts of many of the men is not known." [Source: Michael Valpy, Globe and Mail, November 1, 1999]

Genocide of Young Men in East Timor?

On September 10, a confirmed gendercidal killing took place at Passabe in the enclave of Oecussi. Reporting investigators' findings in February 2000, Mark Dodd wrote in the Sydney Morning Herald: "Evidence gathered so far indicated the victims were mostly men taken on September 8 from villages near Passabe, identified by Indonesian authorities as pro-independence strongholds. According to accounts from independence supporters, between 52 and 56 men were marched across the nearby border into West Timor for registration. Their hands were then bound with palm twine and they were marched a short distance back into East Timor where they were executed." [Source: Mark Dodd, Sydney Morning Herald, February 9, 2000.)

Doug Struck and Keith B. Richburg wrote in the Washington Post, “Jani thought he was safe on the ferry. After three days of terror in East Timor, the boat would take him and two college friends to safety, he thought. Then the militiamen boarded. No young men may leave East Timor, they announced as the boat prepared to depart. Jani, 27, tried to hide; the militiamen caught his friends. "Are there any others?" they demanded, Jani recalls. "No, no other young men," his friends replied in a last gift of kindness. They marched Armando Gomez, 29, and Armando DiSilva, 30, to the front of the boat and killed them as 200 refugees watched. Gomez's body was dumped into the sea, DiSilva's on the ground by the dock. Jani raced through the boat. "Please help me," he whispered to the other refugees. A woman motioned to him to hide between her and her children. The searching militiamen walked by. [Source: Doug Struck and Keith B. Richburg, Washington Post, September 14, 1999]

On September 24, Amnesty International detailed "credible reports that 35 young East Timorese men were killed on board a ship bound for Kupang from Dili on 11 September. According to an eyewitness account, the bodies of the victims were dumped overboard. Amnesty International has collected accounts of other incidents of East Timorese being beaten and killed on boats leaving Dili." [Source:, Amnesty International, September 24, 1999]

Canada's ambassador to Indonesia at the time, Ken Sunquist, was among the first foreign diplomats to visit the camps in the West Timorese capital of Kupang, home to more than 100,000 refugees fleeing anti-independence militias." He said, “The refugee camps themselves are filled overwhelmingly with women and children, so we're wondering where the men are, whether they've been segregated elsewhere, whether they're up in the hills in East Timor or if there's some more sinister explanation. We tried to ask these questions on several occasions but it's clear that the people felt we were putting them at risk even talking to them. There were lots of police around everywhere we went." [Source: Paul Dillon and Jeff Sallot, The Globe and Mail, September 16, 1999]

Later Sunquist said: “The camps have women and children but no men. What's happened to those men? You can either take one approach, which is most of them went up in the hills to fight. That is probably true for a lot of them. A second one is that they were segregated. There's a lot of reports that say the men were segregated. ... In fact, from what we've now heard, there are some camps along the border which are almost entirely male. So maybe the husbands, fathers, brothers, were segregated and are sitting in camps by themselves. I really hope that's true. And then there's the third one, that they were killed. No one, I mean, not anyone is willing to say that they were killed, because they don't know what happened to them. The wives don't know. They know they are missing. [Source: Richard S. Ehrlich, Laissez Faire City Times, September 27, 1999]

Refugees Fleeing Violence After the Referendum

Some 250,000 East Timorese fled to West Timor to escape the militia violence and 40,000 to 50,000 became refuges forced to live in squalid conditions. In some cases the camps were controlled by militia members, who in some cases told refuges they had to pledge allegiance to the Indonesian flag or they would be beheaded or disemboweled. Young men were often forced to join the militias.

One refugee told the Washington Post, "We left about 1 o'clock in the afternoon. We ran. We only had about 15 minutes, and we took some thing of importance: a little rice, some dishes, some clothing for the children." He said they hiked two hours to a seminary. They built a hut with palm leaves and ate the rice potatoes and manioc paste they grabbed. A week later the Indonesia military showed up and opened fire. Most of the refugees escaped into the forest. Some ended up at refugee camps in West Timor and even Darwin Australia.

The situation in the camps of West Timor, to which much of the Timorese population had been forced to live in by Indonesian forces, was also harsh. John Aglionby wrote in The Guardian of the "refugees" being "herded, sifted, and cut off." He cited one witness's testimony that "Many of the men are [being] 'taken away for questioning' ... The women have no idea what happens to their husbands. Many have not returned." One woman reported a militia camp guard's comment that "You may have got your country but it will be a land full of widows." (The Guardian, September 10, 1999.) A detainee who returned safely, Domingos Dos Santos, told Agence France-Presse that "pro-Indonesian militias were hunting down male refugees and planned to kill them all." ( BBC Online, October 3, 1999.) On October 10, Timorese leader Xanana Gusmao spoke of "more than 230,000 East Timorese [having] been taken to camps in Atambua, Kefa, Kupang, Alor, Wetar and Kisar where the men were selectively murdered, leaving only women, children and the elderly." (AFP, October 11, 1999.) [Source:]

As of March 2001, 120,000 East Timorese still filled camps abandoned by the United Nations.

Justice for the Killings After the 1999 East Timor Referendum?

In AFP reported: “Militias under Eurico Guterres ruled the Dili streets in the days following the independence vote, killing civilians and torching buildings. In 2006, he was sentenced to 10 years in prison for human rights violations. The conviction was overturned by the Indonesian Supreme Court in April 2008 year and he was released to pursue a political career in West Timor. [Source: AFP, August 29, 2009 ***]

“A reconciliation commission established jointly by East Timor and Indonesia found last year that while gross human rights were committed by Indonesian forces, there should be no more trials and no further arrests. East Timorese President Jose Ramos-Horta, a Nobel Peace laureate who devoted his life to ending the Indonesian occupation, has been outspoken in his support of amnesty as a prerequisite for normalising ties with Indonesia. In a recent interview, he told Foreign Policy magazine: "Let bygones be bygones. Let us not forget the victims and heroes, but let us forgive those who did harm." ***

“Those who remain unpunished shouldn't sleep easy just yet though. Militia leader Martinus Bere was apprehended in East Timor on August 8, more than five years after he was indicted for his role in the Suai church massacre of September 6, 1999, when up to 200 people were killed. There could be more arrests like this in the future, says Louis Gentile, representative of the UN High Commissioner for Human Rights. "There is an increasing recognition (around the world) of the principle of universal jurisdiction, which means that someone who has committed crimes of that gravity could be prosecuted in any jurisdiction that recognises this principle," he said. Ramos-Horta's forgive-and-forget pragmatism also has its detractors in parliament. ***

Ellen Nakashima wrote in the Washington Post, in interviews in villages across East Timor “the victims' families said they wanted to know the truth. Who murdered their relatives, who gave the orders, where are the bodies? But the truth, they said, is not sufficient. The survivors, who in some cases live near the people who burned their houses or carted away the bodies, hunger for justice: They want the killers charged and tried in an impartial court of law. The families' insistence on prosecutions puts them at direct odds with their government, whose leaders, veterans of the 24-year struggle for independence from Indonesia, now want friendship with the former occupier. "They're playing word games," said an indignant Rafael dos Santos, the Liquica parish priest in 1999 and now a Catholic school principal in Dili, the capital. "A crime is a crime. Justice is justice."[Source: Ellen Nakashima, Washington Post, September 16, 2005]

How Many Died in the Violence After the 1999 East Timor Referendum? Thousands? reported: “Were the atrocities that took place in East Timor in September-October 1999 on a "genocidal" scale? The consensus position of internatonal commentators has been "no" — that in fact, the deaths amounted to no more than a few hundred people, perhaps only "dozens," as an Associated Press report claimed in mid-2000. Around 1,500 dead Gendercide Watch considers these estimations to be highly suspect, and deriving in part from the desire of the international community (especially the U.N.) to avoid blame for its failure to intervene promptly in the slaughter and destruction. The evidence is threefold that killings occurred on a much larger scale than has been generally recognized. First, independent investigators, operating with very few resources, have uncovered subsantially greater evidence of mass killings than has the tiny group of investigators dispatched by the United Nations — but most death-count estimates have been based on the U.N. efforts. Second, there is strong physical, eyewitness, and circumstantial evidence of bodies being disposed of in large numbers at sea, or otherwise destroyed and hidden by Indonesian forces and Timorese militia-members. Last, and most significant, tens of thousands of Timorese remain "missing" and "unaccounted for" a year after the horror — though this subject has attracted no attention in international media for many months. The physical evidence. The possibility of turning up extensive forensic evidence of the atrocities has diminished drastically since September 1999, as a result of two factors: the apparently systematic attempts by Indonesian forces and militia to destroy such evidence; and the pathetically inadequate efforts by the U.N. to investigate atrocities on the ground. [Source: |+|]

“Reports of the destruction of evidence are widespread. According to Australian doctor Andrew McNaughtan, "It is very clear that there has been a very organized, orchestrated, systematic cleanup of bodies" by Indonesian forces. ( Kyodo November 2, 1999.) Australian army lawyer Jens Streit told The Washington Post in October 1999 that "The great lengths the militias have gone to to hide and destroy the bodies makes it very difficult for us to figure out what happened. We have eyewitness accounts, but other than things like shell casings and blood stains, we don't have a lot of physical evidence. ... The Indonesians are extremely concerned about saving face. They want to be able to deny any of this happened" (Rajiv Chandrasekaran, Washington Post, October 22, 1999). It is also certain that many victims were trucked across the border to West Timor and buried there: in late November 1999, 25 bodies were discovered by Indonesian non-governmental investigators in three mass graves on the western side of the border. Recall also the frequent testimony, already cited, of young men being taken out to sea to be killed, and their bodies dumped overboard. |+|

“As for international investigations, in marked contrast to the hundreds of forensics experts who were rushed to Kosovo in the wake of the Serb killing campaign earlier in 1999, only a handful of investigators were made available by InterFET (the International Force in East Timor), most with no forensics training. " The limited international efforts were cast into sharp relief by the work of the East Timor Human Rights Commission, a group of 79 Timorese volunteers, mainly students, who on their own "found evidence of 364 recent killings in Dili" and vicinity alone. Bodies found on beaches were not included in the total. (Paul Daley, "Massacre Evidence Grows", The Age, November 12, 1999). |+|

In a chilling report in the Melbourne Age, reporter Paul Daley wrote that "Evidence of hundreds of killings in Dili alone — and potentially many more at sea — confirms the view of Australian intelligence figures that thousands, rather than hundreds, of East Timorese have died in recent months." Citing "allegations that the Indonesian military (TNI), police and militias killed a large number of East Timorese students aboard a passenger ferry on route from Java to East Timor on 7 September, before dumping them at sea," Daley added: “The allegation is given weight by Australian signals intelligence, which specifically indicates a large number of East Timorese students were killed at sea. The signals intelligence generally points to many other East Timorese being killed on boats — or land — before being dumped into the ocean. The Australian intelligence officers believe the discovery of more than 90 bodies on beaches on the north and south coasts of East Timor in recent weeks, also indicates a large number of people were disposed of at sea. "You have a situation where, in some cases hands and feet were tied, in other cases bodies have wounds or were burnt. It leads to the conclusion that large numbers of East Timorese could be dead — some killed at sea, others killed on land, then burnt and hidden at sea," an intelligence figure told The Age. "This takes some effort and it points to a systematic cover-up." In a subsequent story, Daley cited another intelligence officer who told him that "The bodies found [by InterFET] weren't meant to be found — that is, they were stuffed in drains, dumped in wells, buried in shallow graves and charred in burnt buildings. We believe they are the ones that the Indonesians themselves missed after cleaning up what they thought were all the bodies, before InterFET arrived and while journalists had been forced out of the place." [Source: Paul Daley, The Age, November 12, 1999 |+|]

The voting drive conducted by the U.N. mission in East Timor registered 438,000 Timorese who were of voting age — over 17 — and who expressed a desire to cast a ballot. The U.N. then estimated the total population of East Timor as between 850,000 and 890,000, in keeping with standard "Third World" demographic trends in which 50 or even 60 percent of the population are minors. Thus, the international community never had as clear an idea of the number of Timorese in the territory as at the very point when the slaughter broke out at the beginning of September 1999. In the early days of the September crisis, estimates of Timorese "unaccounted for" ranged from 200,000 to as high as 600,000. In October, José Ramos Horta spoke of the possible "disappearance" of 100,000 people in the territory. As the Indonesian armed forces prepared to depart, many thousands of Timorese subsequently returned from hiding to their shattered communities. But on November 3, the head of InterFET, Maj.-Gen. Peter Cosgrove, told media that "There is a discrepancy, we feel, of about 80,000 [people]. Are these in the hills or just unlocated? We are not sure. There could be more in West Timor than we've found, there could be more in the hills, or in the wider area of the Indonesia archipelago." But he also mentioned "speculation about a fourth fate." Cosgrove, it must be noted, was basing his estimate on a total Timorese population of 800,000 — some 50,000 to 90,000 fewer than the U.N. estimates made at the time of the voter-registration drive. On November 5, The Sydney Morning Herald reported: "Different U.N. officials calculate that the human cost of Indonesia's bloody withdrawal could be close to 200,000." As the East Timor Observatory (a Portuguese body created to monitor the transition process) noted grimly, "Whatever figures are used, the difference is in the region of tens of thousands, probably many tens of thousands. It would be illogical to dismiss the possibility of genocide before finding out what has really happened to all the 'disappeared.'" |+|

If tens of thousands of Timorese are indeed "missing," where might they have gone? One possibility is that large numbers were forcibly dispersed to distant corners of the Indonesian archipelago. Some may simply not have been listed as "accounted for" within East Timor itself. But Dr. William Maley of the Australian Defence Force Academy has been quoted as saying that "a lot" of the missing could have been murdered. He cites the obviously extensive planning that underlay the terror campaign of September as "one reason I think it would have been possible to kill a lot of people in a short period of time. It wasn't just a ragged-edge exercise with a few people running amok because they were disappointed with the result. ... At the early stages of a genocide investigation one does not start with body one and then go on to count a pile of bodies. It's in terms of population estimates and population deficits. If you have a population of, say, 880,000 and then you count everyone and there are only 700,000, that doesn't mean you can explain at this stage what happened to every individual. But it is very strong evidence that something very nasty has happened. People don't disappear into thin air if they are alive." [Source: Brendan Nicholson, The Age, November 12, 1999 |+|]

A snapshot of the quandary was provided by Sydney Morning Herald reporter Lindsay Murdoch in April 2000. Writing from the district of Liquica, 40 kilometres west of Dili, Murdoch noted that "almost every day people trail into the Liquica police station to tell the United Nations police stationed there about new grave sites." According to a U.S. police officer assigned to the force, Alan Williams, "Officially we must stay with the number of bodies that we have actually lifted, but the total number of people killed in this district is much, much higher than that, perhaps even astronomical." [Source: Murdoch, Sydney Morning Herald, April 8, 2000 |+|].

“With most of the physical and forensic evidence of atrocities washed away by monsoon rains, the only feasible way of determining the scale of the killings in East Timor is by conducting a fullscale census of the Timorese population. Such a survey "is necessary and urgent," the East Timor Observatory proclaimed in November 1999. This would take no more effort than the efficient voter-registration drive carried out immediately prior to the plebiscite, which permitted an accurate estimate to be made of the overall Timorese population. |+|

Commission for Truth and Friendship Indonesia-Timor Leste Report on the 1999 Violence

In July 2008, the final report by joint Indonesian-East Timorese Truth Commission blamed Indonesia for the human rights violations in the run-up to East Timor's independence in 1999 and urged it to apologise. President Yudhoyono expressed "deep regret" but stops short of an apology.

According to a 300-page Commission for Truth and Friendship (CTF) report obtained by the Australian newspaper, The Age, and released by Wikileaks: “Indonesian soldiers, police and civilian officials were involved in an "organised campaign of violence” and Indonesian police, army and civilian government officials funded, armed and co-ordinated anti-independence militias that carried out crimes against humanity. It says the Indonesian state bears "institutional responsibility" for atrocities including murder, rape, torture, illegal detention and forced mass deportations. [Source: Wikileaks, July 28, 2008 +]

“While the CTF finds pro-independence groups committed crimes in 1999, the overwhelming weight of evidence is that pro-Indonesian militias were the "primary, direct perpetrators of gross human rights violations". It says the TNI (Indonesian military), police and civilian authorities "consistently and systematically co-operated with and supported the militias in ways that contributed to the perpetration of crimes". The TNI armed the militias, helped co-ordinate and direct their actions, and sometimes participated directly in massacres of suspected independence supporters. +

“The civilian government funded militia groups, even when it knew they had committed massacres. "The provision of funding and material support by military and government officials was an integral part of a well-organised and continuous co-operative relationship, in the pursuit of common political goals aimed at promoting militia activities that would intimidate or prevent civilians from supporting the pro-independence movement," the report says. "TNI and police personnel, as well as civilian officials, were at times involved in virtually every phase of these activities that resulted in gross human rights violations including murder, rape, torture, illegal detention, and forcible transfer and deportation," it says. "Viewed as a whole, the gross human rights violations committed against pro-independence supporters in East Timor in 1999 constitute an organised campaign of violence," it says. "The TNI, Polri (police) and civilian government all bear institutional responsibility for these crimes." As a result, it concluded that "Indonesia bears state responsibility" for gross violations of human rights. +

“Former general Wiranto, who was armed forces chief in 1999, has argued consistently that the upheaval was the result of mob violence. Indicted by UN prosecutors for crimes against humanity, he has never been tried and is a likely candidate in next year's Indonesian presidential election. When he appeared at a CTF hearing in May 2007, he dismissed as absurd allegations that the military had orchestrated the violence. But the CTF, which does not name names and has no power to recommend prosecutions, says the violence was "systematic, co-ordinated and carefully planned". The crimes happened under the watch of BJ Habibe, who was president of Indonesia throughout 1999.

Paul Toohey wrote in The Australian: The truth about Indonesia's role in East Timor's bloody 1999 referendum has been accepted by both sides but it also states the obvious. There was never any question that it would tread softly. After all, it was called the Commission for Truth and Friendship, not the commission for truth. It was set up by the leaders of East Timor and Indonesia not merely to rake over the horrors of 1999 but most of all to find a way forward for two neighbours with a history of bad blood. There was also never any question that the Indonesian military, police and civilian officials — that is, the Indonesian government — would be found responsible for urging and participating in atrocities. For the commission to have concluded otherwise would have rendered the report an embarrassing lie. [Source:Paul Toohey, The Australian on July 18, 2008]

The report recommends no individual receive financial reparation. It suggests, vaguely, that both Indonesia and East Timor employ "collective reparations". One can imagine this would work similarly to the approach taken to Australia's Stolen Generations: no personal payouts but assistance in the form of grants to offer group comfort; counselling, if you're lucky. Maybe tea and biscuit money for survivors to sit around and discuss their grief.

Image Sources:

Text Sources: New York Times, Washington Post, Los Angeles Times, Times of London, Northern Illinois University, Department of Anthropology and Center for Southeast Asian Studies, May 2005 Compton’s Encyclopedia, The Guardian, National Geographic, Smithsonian magazine, The New Yorker, Time, Newsweek, Reuters, AP, AFP, Wall Street Journal, The Atlantic Monthly, The Economist, Foreign Policy, Wikipedia, BBC, CNN, and various books, websites and other publications.

Last updated June 2015

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