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The Indonesian government as of 2009 is smarting over losing control of East Timor in a UN-sponsored plebiscite in 1999, and has repeatedly stated it will not stand for any attempts to break up the country. In December 1999, violence between Christians and Muslims broke out in the Maluku Islands, also known as the Spice Islands. Nearly 10,000 people died during the next two years. Much of that violence was blamed on the Laskar Jihad, a militant Islamic group that wanted to drive all Christians out of the region.

As of 2009 heavy fighting between the Muslims and Christian groups has stopped in the Malukus, but sporadic skirmishes break out occasionally. Violence and unrest can erupt without warning. Sectarian, ethnic, communal (inter-intra group) and separatist strife, and violence are ongoing threats to personal safety and security in various areas, including Maluku (Moluccas), North Maluku, Sulawesi, Papua and West Timor.

The Moluccas or Moluccan Islands are located in the northeast region of the Indonesian archipelago, bordered by the Philippines to the north, Irian Jaya or West Papua to the east, and the Indonesian island of Sulawesi to the west. There are more than 20 large islands in the archipelago, the largest of which include Halmahera, Seram, and Buru, and the province is spread out over great distances of ocean. The population of the entire Moluccas is approximately 2 million, with a large concentration of people in Ambon, capital of the southern region. (Ambon refers also to the island on which the city is located.) The Arabs first brought Islam to the Spice Islands in the 13th century; the Spanish and Portuguese arrived in the 16th century, bringing Christianity with them, followed in the next century by the Dutch.

Most Christians reside in the eastern part of the country. Roman Catholicism is predominant in East Nusa Tenggara Province and in southeast Maluku Province, while Protestantism is predominant in central Maluku Province and in North Maluku and in North Sulawesi Provinces. In the easternmost province of Irian Jaya/Papua, Protestants predominate in the north, and Catholics in the south. (This is due primarily to the Dutch policy--continued by the Indonesian Government--of dividing the territory between foreign Catholic and Protestant missionaries who remain active in many areas of Irian Jaya/Papua.)


In the Moluccas, over half a million people were internally displaced, and thousands forced to convert to another faith, largely because of their religious affiliation. While the underlying causes of the conflict were attributable largely to unresolved grievances and resentment over the distribution of economic and political power between local residents and more recently arrived migrants, the competition quickly took on religious overtones and resulted in the segregation and displacement along religious lines of the population in both provinces. A major factor contributing to the continuation of violence in these two provinces through 2004 was the failure of the Government and security forces to bring the perpetrators to justice, and to prevent the influx of or deport several thousand armed Muslim militants (Laskar Jihad) from Java who joined forces with Muslims in various parts of the two provinces. The presence of these outside forces hindered local reconciliation efforts and peaceful resolution of the conflict.

In January 1999, serious fighting erupted between the Christian and Muslim communities on the Islands. Though there were occasional lulls in the fighting, over the next two years 5,000-8,000 people were killed and 500,000 people displaced from their homes. The conflict divided Moluccans along religious lines, though its origins involve ethnic, economic, and political rivalries also. Houses of worship were pointedly targeted and more than 100 mosques and churches have been destroyed or damaged. During the first 15 months of the crisis, the fighting between the two groups, largely cyclical reprisals, resulted in more or less equal numbers killed on each side.

The apparent spark that led to the outbreak of fighting is reported to have been an argument in Ambon city between a Christian public transport driver and at least one Muslim passenger. The argument soon deteriorated into a brawl and then spiraled into several days of mob violence.28 The fighting then spread to other islands, thus beginning the cyclical pattern. Much of the initial anger on the Christian side was directed at the Bugi, Butonese, and Makassari immigrants rather than Moluccan Muslims. In North Maluku, the fighting was not initially along religious lines at all but was between rival supporters of the two leading sultans in the region.

In the Moluccas, early December 1999 saw a continuation of the sporadic violence that began in late November. One incident that reportedly encouraged the involvement of the Jihad was a particularly bloody battle in December 1999 on the island of Halmahera in the north in which 500 Muslims were killed and the district "cleansed" of 10,000 others who were forced to flee. This incident, as one report notes, "was pivotal in galvanizing national Muslim calls for Jihad." In addition, attacks on the islands of Kesui and Teor brought with them reports of forced conversions to Islam. These forced conversions are reported to have continued through the end of the month. Meanwhile, Ambon Island and other parts of Maluku became much calmer as the month progressed. Initial fears of reprisal attacks during the Christmas and Idul Fitri holidays gave way to a cautious calm as people of both religions celebrated their holidays quietly and in relative peace.

Religious intolerance, especially on the part of extreme Muslims towards religious minorities, including Christians, increasingly was evident and became a matter of growing concern to many religious minority members and Muslim moderates. The lack of religious tolerance continued to manifest itself in scores of violent incidents in the Moluccas, including forced conversions and killings of individuals because of their religious affiliations. There were credible reports that several hundred Muslims were forced to convert to Christianity in North Maluku in early 2000 and thousands of Christians were forced to convert to Islam in North Maluku and Maluku provinces during 2000. Religious intolerance also manifested itself in numerous attacks on churches in various locations, ranging from minor damage to total destruction. Mosques also were attacked in Maluku Province. While in the past the victims in the Moluccas conflict were equally divided between Christians and Muslims, most of the estimated 1,200 victims during 2000 were Christian.


Witnesses testified to human rights groups of incidents when active duty and retired military personnel participated in or stood by during the torture or executions of Christians who refused to convert to Islam in the Moluccas. These incidents reportedly occurred during the period covered by this report in Ambon, Keswui, Buru, Seram and other parts of Maluku Province, as well as in February 2000 in Lata Lata, North Maluku Province. Witnesses and victims also testified to human rights organizations that active duty military and police officials stood by while members of one religious group raped or mutilated members of another faith. Mass forced conversions and circumcisions of Christians in the Moluccas occurred during the period covered by this report, and witnesses and victims alleged that active duty military and police personnel were present, but did nothing, during some of these incidents.

Despite the imposition of a state of civil emergency in June 2000 and promises to deport all non-resident provocateurs, the Government failed to halt the violence in Maluku Province, largely because of weak local government leadership and interservice rivalry between elements of the security forces.

During the period covered by this report, there were reports of beatings of Christians by Muslim police officers and of Muslims by Christian police officers in Maluku Province. There also were reports of Muslim military personnel beating Christians in the Moluccas. For example, on October 16, 2000, in the Christian area of Susupu, Halmahera (North Maluku) the leader of the army unit stationed there allegedly hit a Christian leader in the head with a pistol, fired warning shots into the air, and threatened to kill him and other Christians if they did not cooperate with the security forces.

In June 2000, President Wahid declared a state of civil emergency (one step below the imposition of martial law), giving the military and the police wide room to act, though under civilian command. However, this apparently did little to change the situation on the ground. Many speculated that Wahid was reluctant to take firm action against the militant groups because of his own shaky position, since a significant portion of the country's population is sympathetic to the plight of the Muslims on the Islands. Another concern was that if the Laskar Jihad fighters left the Moluccas, they would take their fight elsewhere in Indonesia and pose an even greater threat.

From July to November 2000, the Government largely was ineffective in deterring interreligious violence that led to over 1,000 deaths, thousands of injuries, and tens of thousands of displaced persons in the Moluccas. Enforcement of the law against criminal violence deteriorated, encouraging religious groups purporting to uphold public morality to act with growing impunity. In some incidents security forces took sides in the conflict and participated in the violence; in others the forces stood by while Christian and Muslim civilians battled one another. According to many Christian leaders, the anti-Christian sentiment behind the violence in the Moluccas and elsewhere is not new, but the failure of the Government to punish the perpetrators associated with such acts is new. They claim that such impunity has contributed significantly to the continuation and spread of the violence. However, starting in December 2000, the security forces in Ambon started to act more objectively, often stemming attacks by one militant religious group against a civilian population of another faith. However, perpetrators--Laskar Jihad members in particular--rarely were detained and when they were, they typically were released after supporters rallied in demand of their release and threatened police. In addition the Government failed to suppress or respond to most cases of violence and did not resolve fully the many cases of attacks on religious facilities that occurred during riots. In many cases, the Government did not investigate such incidents at all.

In the Moluccas, both Christians and Muslims alleged that police and military personnel were not always neutral and often sided with coreligionists in the communal conflict. In Maluku Province, Christian sources continued to allege that Muslim security forces often would fail to intervene to protect Christian areas that were attacked by Muslim militia. For example, predominantly Muslim units dispatched from Java and Sulawesi allegedly sided with Muslim vigilantes and used excessive force against Christians. In other instances, Muslims claimed that Christian security forces would not defend Muslim areas attacked by Christian militia. Muslims in Ambon claimed that members of the predominantly Christian police force sided with their coreligionists. However, there was no evidence to suggest that the security forces, as an institution, supported either group. Some individuals and some units occasionally sided with their coreligionists, but their actions appeared to be random and contrary to orders.

19 January 2001 marked the two-year anniversary of the conflict in Maluku. On Ambon island, this date set off an immediate upsurge in violence.On January 21 and 22, 2001, a joint military/police force created to deal with "rogue" police officers and militia members clashed with Muslims in Ambon, killing 10 Muslims, including three Muslims that had attacked a military patrol; two police officers also were killed. Muslim leaders criticized the joint force for acting in response to pressure by domestic and foreign Christians. Several hundred police officers themselves were attacked, and some were killed because of their religion; hundreds of police members and their families and numerous other government officials are among the country's internally displaced persons (IDP's). By the end of the month, the increase in violence had been reduced to isolated sporadic incidents.

In February 2001, North Maluku Province authorities detained, questioned and then expelled three foreign Christian missionaries and several Muslim teachers of Pakistani nationality. The province was under a state of civil emergency at the time (and throughout the period covered by this report). The Governor required both foreign and domestic groups from outside the province to obtain prior permission to enter the province and forbade entry if he believed the presence of an outside group might trigger more sectarian violence.

March 2001 was a relatively calm month in Maluku, although tensions still remain just below the surface. The Hotel Wijaya incident of the previous month, in which Indonesian police and military units fought each other, gave way to a sense that both the police and the military were taking the matter seriously and were trying to follow up in a more professional manner than has been the case in the past. On the negative side, there was evidence that Laskar Jihad was on the move again and may be trying to consolidate their power base among an increasing number of Muslim communities on the island. They have also been seen in Ambon attempting to purge prostitutes and other "bearers of vice" from Muslim sections of the city. The result has been confrontation with Ambonese Muslims, who are seen to be much more tolerant of such elements in thier midst. Finally, Ambon was rocked by the premature death of Christian fighter-turned-grassroots peacemaker Agus Wattimena, who was alleged to have been murdered at home by his wife.

In May and June 2001, there was renewed violence, incited by the continued presence and activity of armed militant Muslims from outside the province.

Tensions in Maluku continued during the month of May 2001, with a new outbreak of violence and a change in the way violent acts were perpetrated. Much of this was at the hands of the hard-line Muslim Laskar Jihad group, which began employing more terrorist-style tactics, the sweeping of international organizations' vehicles for Christians and targeting specific Muslim communities they deemed had gone "off message."

In June 2001, the security situation in Maluku worsened visibly. Tensions escalated with a new outbreak of violence and a shift in the way violent acts were perpetrated. Much of this was at the hands of Laskar Jihad, which began employing more terrorist-style tactics by sweeping international organizations' vehicles for Christians and targeting specific Muslim communities they deemed had gone "off message". The military responded to this new form of violence in an equally heavy-handed manner. By mid-June, the military's Joint Battalion attacked and destroyed an "illegal" radio station owned and operated by Laskar Jihad. The Joint Battalion then launched a weapons sweep at a Laskar Jihad health clinic, killing or injuring a number of civilians. The public reaction from both Christian and Muslim communities was one of outrage. In response, the military hastily recalled the regional military commander and assigned him to another part of the archipelago in what was seen as a demotion.

During July 2001, the sporadic violence that characterized the months of May and June continued, especially in Ambon City. A 6:30 p.m. curfew was imposed and gunfire and/or bombs can be heard regularly at night. In spite of this, neutral spaces around the city continue to be used by both communities during the daylight hours. Recent violence in the area surrounding the airport has reduced the perceived feeling of security that visitors to the province had previously enjoyed.

In an apparent effort to destabilize communities, bombings or bomb threats increased during August 2001 in or near areas frequented by Muslim and Christian traders and patrons. Fortunately, trade and contact between the two communities has not been seriously inhibited by these incidents.

The sporadic bombing of neutral locations frequented by both Muslims and Christians that began in August continued into September 2001. However, members of both communities expressed their defiance of such actions by quickly returning to their trading or other integrated activities soon after the bombings took place. There appeared to be a new split within Ambonese society - in particular, between the elite (political and economic) trying to control when and where such trading activities take place, and the grassroots - who openly defy the elites in order to carry on with their daily activities as they see fit.

The situations in North Maluku stabilized due in large part to effective local government leadership that enforced the ban on entry by outsiders and administered justice to the perpetrators.

The events of September 11 appear to have had little impact on the situation in Maluku to date. Laskar Jihad, a hard line Islamic group, has been quiet on this subject within the province and none of the hard line Christian groups have made any related statements. While international NGOs remained cautious and continued to monitor the situation at month's end, there was no indication that they would curtail their activities.

The situation in Maluku remains highly conflicted during October 2001, with sporadic bombing of locations in or near neutral transaction points frequented by both Muslims and Christians. As has been the case in the past,, members of both communities expressed their defiance of such actions by quickly returning to their trading or other integrated activities soon after these events took place. In an effort to reduce the risk to people and their assets in these locations, the Mayor of Ambon moved trading points from the neutral areas considered to be most at risk to other neutral areas that are less frequented but under tighter control by the security forces. The reaction of traders was one of anger at not having been consulted and at the prospect of reduced sales due to lighter foot traffic in the alternative locations.

Tensions in Ambon continued with almost daily incidents of shootings, bombings, and other disturbances. At the end of November 2001 the Christian community held a three-day mass prayer vigil, which brought all commercial, governmental and transport activity to a halt. Christians viewed the vigil as an attempt at introspection in response to the continuing violence; Muslims regarded the action as holding the provincial government and the city hostage.

There were no reports that the Government was directly involved in the forced resettlement of individuals because of their religious affiliations; however, the Government did urge many Christian and Muslim IDP's in the Moluccas to relocate temporarily to designated IDP camps or other facilities. The Government's urging of IDP's to relocate to safer areas is standard policy and appears to have been driven by concerns for IDP safety and welfare. Victims and witnesses reported that some active duty and retired military and police stood by while militia groups forced non-coreligionists out of their communities if they were unwilling to convert. Most of the incidents involved Muslim militia expelling Christians; however, there also were some reports of Christian militia expelling Muslims from certain areas (on Halmahera Island, North Maluku, and on Saparua Island, Maluku).

Conflict re-erupted on the island of Buru, where as many as 300 people where either injured or killed in the sub-district of Leksula on the south coast of the island. The violence lasted for almost three days and was ended when military reinforcements intervened.

The Indonesian government launched peace talks February 11, 2002 in Malino between Maluku's Muslim and Christian communities. These talks were an important step in Indonesia's efforts to end violence, re-establish the rule of law, and provide for reconstruction in the troubled province.

At the end of May 2002 the central government announced the formation of a special operations military command for Maluku to be headed by a two-star general named Djoko Santoso. This command will exist alongside the current Pattimura territorial command and General Santoso will succeed General Mustopo as head of the command. Legal experts and human rights activists have been quick to point out that there is no legal basis for establishment of the special command and that the move was tantamount to declaring martial law.

After three long years of being separated from each other, thousands of Christians and Muslims in Ambon celebrated the signing of the Malino II Agreement by parading together through the streets of Ambon, Indonesia, and crossing freely into each other's neighborhoods. For Malukans, this was a time of great optimism but also caution, with many citing it as a test of the willingness and ability of the police and military to control the violence and refrain troops from becoming involved.

With a week of violence and the death toll at 38, in late April 2004 nationalist Muslims renewed clashes with Christian separatists in Ambon, Indonesia, raising fears the region could plunge back into a civil war similar to clashes that killed 5,000 people three years ago. Controversy grew as the conflict was widely blamed on security forces for not taking preventative measures and appearing unable or reluctant to stop the fighting. Amidst breakdowns in peace talks and anticipated reprisals, officials attempted to restore order by replacing the Maluku Police Chief while deploying hundreds of reinforcements and arresting leaders of the Maluku Sovereignty Front (FKM). Although Ambon asked for humanitarian aid/assistance in ending the conflict, President Megawati's passive stance indicated the unwillingness of the government to upset voters ahead of the upcoming July presidential elections. Despite rumors, the local government did not expect Islamist militia, Laskar Jihad, to be an immediate threat.

Christian separatists and Muslims ended two years of peace with renewed clashes on 25 April 2004, leaving 38 killed and approximately 230 injured in Ambon, Indonesia. Hundreds of buildings were torched and thousands of people fled their homes. Initial violence was sparked when a small Christian separatist movement paraded through Ambon to mark the anniversary of a failed independence bid 54 years ago. On Monday, peace talks between local Muslim and Christian leaders, along with Indonesian police, collapsed after Maluku police and military chiefs prohibited local Muslim leaders from reading a statement on their stance over the violence. The violence has been widely blamed on the police for its poor handling of the clashes, although authorities believe the replacement of the police chief, Brigadier General Bambang Sutrisno, will speed up stabilization ahead of 5 July presidential elections. One hundred paramilitary police have been added to the 400 police and 450 soldiers already sent to the Maluku province to disarm civilians and restore order in conflict-prone areas; although witnesses claim Indonesian security forces have done little to stop the clashes and in some cases have even joined in.

Police have also been conducting house-to-house searches looking for weapons and have arrested 34 suspected separatists, including the wife and daughter of pro-independence leader Alexander Hermanus Manuputty. Manuputty, head of the separatist Maluku Sovereignty Front (FKM), fled to the United States last year after being released from prison, pending an appeal to a four-year jail term that was linked to his campaign for independence. For further security, Maluku's navy base is also prepared to contain the infiltration of the Laskar Jihad, a paramilitary organization threatening to wage a holy war against Christians. Laskar Jihad was reportedly disbanded but its leader told Jakarta news organizations last week he would redeploy fighters to Maluku, if necessary. Many agree the recent renewal of clashes have been the worst since a pact in February 2002 ended three years of sectarian fighting that killed 5,000 people. Indonesia's population is 87 percent Muslim but Christians and Muslims live in roughly equal numbers in the Malukus.

In 2005, several shootings, bombings, and small-scale communal clashes that killed between 10 to 15 people occured in Maluku. On Tuesday February 12, 2005, unidentified gunmen on three speedboats attacked a karaoke house on the coast of Maluku, killing 2 people. On Thursday May 5th, police in Ambon arrested and held Semmy Waeleruny, the Secretary-General of the Maluku Sovereignty Front (FKM), a separatist group, on the suspicion that he was plannig more subsersive activities and attacks. On Monday May 16, 2005, a bombing attack on a police post in Maluku by local Muslim militants killed 6 policemen and 2 civilians. In 2005, 15,788 internally displaced families in Maluku were still attempting with government assistance to return to their places of origin or relocate outside of their refugee camps.

Despite the occurence of attacks and continuing separatist and para-military activities, in the 2005 the security situation in the Maluku Islands improved, prompting the Indonesian government to withdraw 3,000 troops stationed there from around Indonesia. As of 2006, it appears that the conflict in Maluku has stopped. However, on April 25th, 2007, Maluku Christian separatists fighting for an independent South Maluku Republic unfurled the utlawed flag of the South Maluku Republic, which was crushed shortly after it was proclaimed in 1950, in three different locations in Maluku's provincial capital, Ambonin. On June 29th, 2007 separatist protestors staged a surprise protest in front of Indonesian President Susilo Bambang Yudhoyuno in , unfurling the outlawed flag before him.

On Satruday February 2nd, 2008, local police in Central Maluku and Inodnesian military stationed there clashed, killing 2 police officers and 1 soldier, and destroying 56 police houses and damaging 11 police cars. On Monday morning November 3rd, 2008 three low-magnitude explosions rocked North Maluku near the residence of the North Maluku governor, the office of the North Maluku regional government, and the building of the North Maluku Regional Legislative Assembly (DPRD). On Tuesday, December 9th, 2008 a riot in the city of Masohi in Central Maluku destroyed several dozen builings 67 houses, and injured over 5 people.

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