CHRISTIANS AND MUSLIMS IN INDONESIA; HISTORY, RELATIONS, VIOLENCE

CHRISTIANS IN INDONESIA

Muslims at the Catholic Monastery of Gedono

Muslim–Christian relations in Indonesia have been strained since the colonial era. Although the Dutch authorities did not actively promote conversion, they allowed Christian missions to operate freely among non-Muslims. Where Muslims and Christians lived separately—on different islands or in distinct regions—relations were generally peaceful. However, beginning in the 1970s, large-scale migration, especially of Muslims from Java, Sulawesi, and parts of Maluku Islands into previously Christian-majority areas such as Kalimantan, Sulawesi, Maluku, and West Papua, altered the religious balance and created new inequalities in economic, ethnic, and political power.

The collapse of the New Order intensified these tensions, leading to outbreaks of violence in places like Ambon and other parts of Maluku and Sulawesi. Weakening control by military commanders over both Muslim and Christian forces in the outer islands further contributed to instability. Historically, Christians tended to remain politically cautious and less organized at the national level compared to Muslims. Yet they have held a disproportionately high number of influential positions in government, the military, academia, and business, partly due to their strong emphasis on modern education. Christian schools and universities have long been prestigious, educating many members of Indonesia’s elite, including non-Christians. Major national newspapers such as Kompas and Suara Pembaruan also originated from Catholic and Protestant communities. These patterns have caused some resentment among Muslims, especially given Christianity’s historical association with Dutch colonialism and foreign missionaries, as well as its connections to prominent Chinese Indonesian communities.

During the New Order period, religion became politically sensitive, as those without an officially recognized faith were often suspected of Communist sympathies. This led to widespread conversions, particularly in Java, where many people adopted Christianity. Followers of indigenous belief systems also came under pressure. In regions like the interior of Kalimantan and Sulawesi, some communities converted to world religions, while others sought official recognition for restructured traditional faiths through political advocacy. Among the Ngaju Dayak, for example, the belief system Kaharingan was eventually classified under the Hindu-Buddhist category, despite being distinct from both.

Anti-Christian sentiments are still pronounced in some places. In the mid-2000s, a notice on a bulletin board at a Muslim school in Java read, 'Beware of the dangers of Christianisation in Indonesia.' It claimed that 15 million Muslims had converted to Christianity between 1956 and 2004, and that in 2004, 'they intend to take the presidency'. Anti-Christian rhetoric often emphasizes perceptions among hardliners that political and economic influence held by minorities was disproportionate. These sentiments have arisen at times, particularly during the violence during the fall of Suharto in the late 1990s, when Chinese Indonesians were frequent targets. [Source: Fergus Jensen and Agustinus Beo Da Costa, Reuters, November 5, 2016]

Violence Between Christians and Muslims

Locations of ethnic violence in Indonesia, with violence between Christians and Muslims mainly on Sulawesi and Maluka Researchgate

Between 1949 and 1996 an estimated 50 Christian churches were burned down in all of Indonesia. In 1998, more than 200 were burned down. The are two major zones of conflict between Muslims and Christians: the area around Poso on Sulawesi and Ambon in the Molucca Islands.

Muslim-Christian relations have been tense since colonial times. These tensions were exacerbated under Suharto by the transmigration program, which brought large numbers of Muslims to previously predominately Christian islands and regions. The end of the Suharto regime in 1998 led to an uncorking of tensions. A lack of authority by commanders over Muslim and Christian troops in the outer islands has made the problem worse.

Conflicts between religions have often had more to do with class differences, particularly between the bureaucratic class and villagers. A key characteristic of Suharto’s New Order regime was the prevalence of security and order throughout the nation. Any outbreak of violence between ethnic or religious groups was quickly and sternly repressed. Tensions simmered below the surface, however.

Sporadic incidents had already begun in 1996 when the New Order still appeared quite solid, with church burnings in such places as Pasuruan (in Jawa Timur) and Tasikmalaya (in Jawa Barat). The scale and geographic spread of violence ramped up significantly, however, following Suharto’s resignation, as the national government became preoccupied with the political transition and security forces could no longer repress long-simmering local grievances.

Violence Agaisnt Christian Chinese

Much of violence against Christian has been directed at Christian Chinese. Tens of the thousands of Chinese died in 1965 during the anti-Communist purges of 1965 that left between 300,000 and 1,000,000 Indonesians dead. Communists. Even so most of the dead were indigenous Indonesians. In December 1965, after a failed communist coup in September 1965, mobs were engaged in large-scale killings, most notably in Jawa Timur Province and on Bali, but also in parts of Sumatra. Members of Ansor, the Nahdatul Ulama's youth branch, were particularly zealous in carrying out a "holy war" against the PKI on the village level. Chinese were also targets of mob violence.

Estimates of the number killed — both Chinese and others — vary widely, from a low of 78,000 to 2 million; probably somewhere around 300,000 is most likely. Whichever figure is true, the elimination of the PKI was the bloodiest event in postwar Southeast Asia until the Khmer Rouge established its regime in Cambodia a decade later. [Source: Library of Congress]

distribution of each religious community with significant percentages per district in Indonesia based on the results of the 2010 census

Anti-Chinese riots in Medan, Sumatra in 1994 left one man dead and alarmed Chinese businessman throughout Indonesia. An ethnic Chinese factory owner was pulled from his car and stoned and beaten death as he tried to protect his factory from thousands of laborers who protesting the mysterious death of a union activist. Thousands of looters with machetes and iron picks laid to a shopping mall owned by Chinese. Many Chinese n Indonesia saw this as an early warning and they began moving their assets to safer havens such as Singapore, and Australia.

In May 1998, riots broke out in which hundreds of Chinese stores were burned and Chinese women were raped and murdered. When many Chinese Indonesians fled the violence, the subsequent capital flight resulted in further economic hardship in a country already suffering a financial crisis. By 2005 many had returned, but the economic and social confidence of many Chinese in the country was badly shaken by the experience.

Christian-Muslim Violence After the Fall of Suharto

After Suharto’s fall in 1998, ethnic and religious conflict erupted in several regions. Security forces were initially ineffective in regaining control because the police, poorly trained, poorly equipped, and understaffed, were ill prepared to handle large-scale unrest. The TNI (Indonesian military), stung by accusations of human-rights abuses, and resentful of the change in mission responsibility, was reluctant to intervene without a formal request for assistance from local authorities. More than 5,000 people were killed between 1999 and 2002. [Source: Library of Congress *]

Conflict broke out in Maluku Province in 1999 after a seemingly minor clash between a bus driver and a passenger who refused to pay his fare exploded into wide-ranging Muslim–Christian violence in Ambon that quickly expanded throughout the Maluku Islands. In January 1999, following the expulsion of Ambonese gangs from Jakarta to Ambon, as well as the breakdown of informal ethnic power-sharing agreements in Maluku Province, a minor traffic accident in Ambon exploded into terrible and sustained violence between Muslims and Christians in that city. Over the next three years, several thousand members of both communities were killed, and parts of the city became no-go zones for one group or the other. Extremist Muslim groups such as Laskar Jihad—allegedly supported by like-minded senior military officers— flocked to Ambon and played a major role in the dramatic expansion of violence in that city. *

The violence that erupted in Kalimantan Barat was even more horrific, as indigenous (Christian) Dayaks in rural Sambas District went on a rampage against Muslim Madurese in-migrants who had taken a prominent role in local commerce and agriculture. Hundreds were killed, some of their severed heads left on poles as a warning to others, and many houses burned to the ground. *

Islamic militants in Jakarta called for jihad to support their coreligionists on the islands. During the same period, Muslim–Christian violence flared in Tengah, around the cities of Poso and Tentena, where Laskar Jihad and the more sinister Jemaah Islamiyah terrorist group had established a training camp. Hard-line civilian and military sympathizers, who wanted to destabilize the regime of then-President Abdurrahman Wahid, collaborated to organize, train, equip, and arm the Laskar Jihad (Jihad Militia) and arranged the unimpeded transfer of several thousand members of the militia to both Ambon and Poso. This caused a major escalation of the conflict. The government declared a civil emergency, one step short of martial law. At the end of the first decade of the twenty-first century, this conflict continues to fester, with sporadic incidents of violence by one community on the other.

Many of these conflicts appear, on the surface, to be between ethnic or religious communities, particularly Muslims and Christians. However, deeper analysis reveals that very localized struggles over political and economic power are the underlying cause. Unfortunately, these political and economic struggles have often been framed by conflict entrepreneurs as being rooted in ethnic or religious cleavages, making it easier to mobilize communities against one another. External forces have also exacerbated such conflicts. In Ambon, security forces were perceived as taking sides, the army with Muslim communities and police mobile brigades with Christian communities.

Muslim-Christian Violence on Java

In November 1998, five months after Suharto was ousted, after a fight between Christians and Muslims at a Jakarta nightclub, several hundred Ambonese Christians armed with samurai swords battled with Muslims armed with machetes. Six people were hacked to death and 11 churches were burnt down. One Western observer saw a dead man dragged through the streets and one of his killers lick the blood on his machete. Shortly afterwards an argument and streets fight between Muslims and Christians in Jakarta escalated into a street battle that left one person hacked to death and 22 damaged churches. In retaliation Christians burned down six mosques in East Timor.

In Jakarta, gang leaders offered $2.50 of each person wiling of offer their services as "volunteers" (thugs for Muslim youth gangs). In Surabaya a church was burned in retaliation after a dog, reportedly belonging to a Christian, urinated on the wall of a mosque. Churches have were also destroyed on Yogyjakarta

On Christmas Eve 2000, 36 bombs were set off at 11 churches in Riau, Batam and Jakarta and other places across Indonesia that left at least 19 dead and 120 injured. The attacks, which occurred in many cases while the churches were having Christmas services. The bombs used the same kinds of explosives, digital timing devises and detonators and went off minutes apart from each other. These are hallmarks of Al-Qaida-style attacks

Jemaah Islamiyah, the Muslim extremist group behind the Bali bombings in 2002, was also behind the Christmas Eve bombings. The attacks were reportedly ordered by the group to avenge the killing of Muslims by Christians in the Maluku islands and central Sulawesi in 1999 and 2000. Some of the members of Jemaah Islamiyah involved in the Bali bombing were also involved in the church bombings.

Christians and Muslims in the Moluccas

The 2 million or so people in the Moluccas are divided roughly equally between Christians (which include Indonesians and Chinese) and Muslims. Until the beginning of 1999 the two groups lived in relative harmony with one another.

Christianity has a 500 year history in the Moluccas and dates back to when Europeans involved in the spice trade began arriving on the islands. Most the Christians are descendants of people who have lived in the Moluccas since Dutch colonial times. Christianity took hold here because so many Christian Europeans arrived here to make money from the spice trade.

Some Muslims are descendants of people who embraced Islam before the arrival of the Dutch. Most are descendants of Muslims from elsewhere in Indonesia that came to the Moluccas. Many are settlers or relatives of settlers who arrived relatively recently from other islands in Indonesia. A few are descendants of offspring of indigenous Malays and black slaves brought to work on the plantations by the Dutch.

History of Christians and Muslims in the Moluccas

The Christians have traditionally had close ties with the Dutch. After the decline of the spice industry they became especially close with the Dutch. They were among the most loyal and trusted and best-educated Indonesians, making up a large share of the Dutch colonial army. They were favored over the Muslims for positions in the colonial government and were the larger of the two groups in terms of population.

After Indonesia became independent, the roles of Christians and Muslims were reversed and Muslims were favored over Christians for good jobs and other privileges. Muslims set up prosperous businesses while Christians were relegated to farming and fishing.

The Christians originally formed a majority on the Moluccas but their dominance was diluted in the 1960s and 70s when the Suharto government encouraged Muslims from other islands to move there. By 2000, the population was about 55 percent Muslim and 45 percent Christian. Even so Christians and Muslims lived in relative harmony. Intermarriage was even common in some places. But all that changed in 1997 and 1998 when the Indonesian economy collapsed and Suharto resigned and buried resentments and animosities came to the surface. Muslims and Christian were involved in a number of disputes over land and intervillage fighting was common, with resulting casualties and burning of property.

Ambonese

The Ambonese live on the island of Ambon and other islands in the Central Moluccas. The are also known as the Alifuru (interior of Ceram), Ambonese, Central Moluccans, the Moluccans, Orang Ambon and South Moluccans (exiles in the Netherlands). Maybe a million people live in the Central Moluccas. The population is pretty equally divided among Muslims and Christians. [Source: “Encyclopedia of World Cultures, East and Southeast Asia” edited by Paul Hockings (G.K. Hall & Company, 1993) ~]

The Ambonese are very ethnically mixed. The Moluccas are near the traditional dividing line between Melanesian and Indonesians peoples and all sorts—Malays, Hindus, Chinese, Europeans, Arabs, other Asians—came to the islands for their spices. Genetic material and cultural traits from all these people have been left behind to varying degrees. ~

They strongest links to Melanesia are found among the Alifuru (Nua-ulu) in the interior of Seram (Ceram). These people were headhunters until they were pacified by the Dutch before World War I and have a secret men’s society, the only such society in Indonesia and something normally associated with Melanesian cultures. In the days, severed heads were said to part of their marriage and coming of age ceremonies. Much of their old ways have ben lost since they converted to Christianity. The culture of the Pasisir people who live in the coastal areas has been influenced much more by outsiders. ~

Muslim and Christian Ambonese

The Muslims and Christians in the Central Moluccas are surprisingly similar culturally. Their ideas about kinship and clan ties are similar, namely that villages or districts are made of several patrilineal clans led by a headman and clan descent is traced to a common ancestor. Marriage customs are also similar. Most are monogamous and in the past were arranged but today are largely love matches that follow two patterns: 1) formal request by the groom’s family, with the payment of a bride price; and 2) elopement. The latter is often preferred because it is way to avoid parental approval and the cost of a formal wedding. Divorce is rare among both Christians and Muslims. [Source: “Encyclopedia of World Cultures, East and Southeast Asia” edited by Paul Hockings (G.K. Hall & Company, 1993) ~]

Ambonese Christians and Muslims have incorporated elements of ancestor worship and each other’s religions into their faiths and excluded members of other ethnic groups from their churches and mosques in an efforts to ensure ethnic harmony of the islands. Contrary to this effort has been efforts by conservatives in each faith to purify their religion and get rid of non-Christian and non-Muslim elements from the respective faiths.

In the Ambonese belief system ancestors are called upon for blessings and invited to villages ceremonies and incorporated into concepts of salvation and the afterlife. There are also Christian and Islamic devils and spirits that cause illness and bring misfortune. At funerals there are often non-Christian and non-Muslim rituals to pacify the spirit of the deceased. Spirits and evil forces are linked with concepts of disease and health although generally Ambonese Western-style doctors before traditional healers.

Anti-Christian Protests in the Indonesia in 2016

In November 2016, large-scale protests in Jakarta highlighted rising anti-Christian sentiment as hardline Muslim groups mobilized against the city’s governor, Basuki Tjahaja Purnama, an ethnic Chinese Christian. Demonstrators accused him of insulting the Quran and demanded his removal from office, turning the issue into a broader religious and political flashpoint.[Source: Fergus Jensen and Agustinus Beo Da Costa, Reuters, November 5, 2016]

The protests, which drew tens of thousands, were fueled by conservative groups that framed Purnama’s candidacy as unacceptable on religious grounds. A Quranic verse—often interpreted by some as discouraging Muslims from choosing non-Muslim leaders—was widely invoked to rally opposition. Although Purnama later apologized and clarified his remarks, many hardline organizations continued to portray him as having committed blasphemy, intensifying public anger.

While much of the demonstration remained peaceful, tensions escalated by evening. Clashes broke out between protesters and security forces, resulting in injuries, property damage, and at least one death. In parts of North Jakarta, where many religious minorities live, unrest took on a more targeted character. Some Chinese-owned shops and businesses closed out of fear, while security was increased around non-Muslim institutions such as temples and schools.

Hardline groups warned that further demonstrations would follow if legal action against Purnama did not proceed. Their stance underscored the growing influence of conservative religious movements willing to use mass mobilization to pressure political outcomes. For many observers, the episode illustrated how religious identity—especially anti-Christian sentiment—could be leveraged to shape public opinion and destabilize Indonesia’s traditionally pluralistic political landscape.

Image Sources: Wikimedia Commons

Text Sources: “Encyclopedia of World Cultures Volume 5: East / Southeast Asia:” edited by Paul Hockings, 1993; National Geographic; New York Times, Washington Post, Los Angeles Times, Lonely Planet Guides, Library of Congress, Smithsonian magazine, The New Yorker, Time, Reuters, AP, AFP, Wikipedia, BBC, CNN, and various books and other publications.

Last Updated December 2025