SUMMARY
After more than three decades of authoritarian rule, Indonesia´s transition to democracy in the 1990s brought about drastic political change. Tensions quickly flared up in the country, triggering ethnic, religious and territorial conflicts. Violent fighting occurred between ethnic and religious groups, as well as between the Indonesian government and secessionist movements; moreover, civilians were often targeted by national security forces, rebels and Jihadist organizations and, over the years, constituted a significant share of the overall casualties. Nevertheless, the last decade has been characterized by relatively low levels of organized violence, most of which has had to do with the territorial conflict over the region of West Papua, fought between government forces and separatist rebel group OPM.
Since 1989, Indonesia has experienced the intrastate, non-state and one-sided categories of organized violence, as defined by UCDP.
2025
The level of violence in Indonesia increased in 2025, following the broader pattern of a slow and slight increase over the last ten years. The ongoing conflict in West Papua between the Indonesian government and OPM was the main cause for this increase, as it reached the highest level of recorded fatalities since the conflict was first recorded by UCDP. The conflict remains localized to West Papua. Both the Indonesian government and OPM continued to engage in violence against civilians. Violence perpetrated by the Indonesian government against civilians remained at low levels, although with a small uptick since 2024. The one-sided violence perpetrated by the OPM, on the other hand, increased slightly compared to last year, while still remaining below the highest recorded level of 2023. Almost all one-sided violence took place in West Papua. No non-state dyads were active in 2025 in Indonesia.
1989-2024
Since 1989, Indonesia has seen fluctuating levels of organized violence, with three peaks and a high plateau in terms of the number of fatalities.
The first peak occurred in 1991, mainly as a result of extensive one-sided violence employed by the Indonesian government, carried out in the regions of Aceh and East Timor, where rebel groups aspired to create separate states. Subsequently, authorities targeted suspected supporters of the Acehnese rebel group GAM, and both regions saw attacks on peaceful protesters. In fact, the surge in fatalities was caused by one incident in particular, when more than 270 pro-independence demonstrators were killed in East Timor in the so-called Santa Cruz massacre.
Between 1992 and 1996, the number of fatalities dropped to low levels, although the country still experienced intermittent bouts of violence. The state-based conflict over the status of East Timor continued, but with low fatality numbers, and during this period, the conflict was only recorded as active in 1992. There was also some bouts of one-sided violence, carried out by the government in Aceh, where GAM was slowly picking up its stride. This lull came to an end in 1997, when organized violence in general, and non-state conflict in particular escalated and a second peak was recorded. This development was a direct consequence of a dramatic uptick in fighting between the Dayak and Madurese ethnic groups, which emerged in a context of great economic and political fragility for Indonesia. The fighting took place mostly in Western Kalimantan, where several clashes caused more than 350 fatalities during the year.
After a lull in 1998, levels of violence surged drastically in several parts of the country in 1999, and the highest peak in the entire time-period was recorded. The magnitude of this peak was a result of escalations in all three types of violence simultaneously. Both one-sided violence and non-state conflict saw its highest peaks to date, with close to 1000 fatalities in the former category, and almost 700 in the latter. Of the fatalities in one-sided violence, a majority were killed by the Indonesian military and allied militias in East Timor, in a violent campaign aimed to discourage the population from coming out to vote in a UN-organized referendum on independence. Developments in non-state conflict, for its part, were mainly driven by the eruption of a conflict between Christians and Muslims in the Maluku islands, as well as sustained fighting between [Dayak and Malay (Indonesia) on the one side, and Madurese on the other. This conflict was closely tied to the previous one, pitting the Dayak and Madurese against each other, but in 1999, the Dayak formed an ad-hoc alliance with the Malay (Indonesia) community. This conflict was mainly played out in West Kalimantan. Less, violent, but still causing close to 200 fatalities, the state-based category saw escalating levels of violence in the conflict over Aceh.
After the dramatic peak of 1999, violence de-escalated somewhat the following year, but remained on a high plateau through 2000-2004. It was developments in non-state- and state-based conflicts that caused the continued high levels of violence, whereas one-sided violence continued to be carried out, but on a smaller scale. In 2000-2001, the trend was driven by high fatality numbers in non-state conflict, as the bloody conflict between Christians and Muslims in the Maluku islands continued, and a new bout of violence in the Dayak –Madurese conflict erupted. At the same time, fighting in the state-based conflict between the government and GAM over the status of Aceh started to really take off, with violence reaching new heights every year from 2000 through 2004, when almost 1000 fatalities were recorded. The most dramatic escalation followed the failure of peace negotiations in 2003, after which the region was put under military emergency by authorities in an attempt to eradicate GAM guerrillas.
Since 2004, the situation in the country has remained far more stable, with relatively low levels of organized violence. The majority of fatalities during this period was a result of the intrastate conflict in Ache and, more recently, of fighting in the conflict between the government and OPM over the status of West Papua. Indeed, since 2009 incidents of state-based violence occurred exclusively in the West Papuan context, as fighting with GAM significantly decreased after a peace agreement was signed in 2006, eventually stopping altogether three years later.
After a relatively peaceful period following the peace agreement, the conflict over West Papua reemerged and was recorded as active again in 2018 and 2021. In 2018, the situation deteriorated when the OPM carried out an attack on construction workers in the Papuan highlands, killing at least 17 people. The escalation in 2021 occurred after rebels killed an intelligence chief, prompting a presidential order to the security forces to hunt down and kill all OPM insurgents. Organized violence in the state based conflict remained at a similar levels in 2022 and was recorded as active in the UCDP data for the third time since 2006. State-based violence occurred exclusively in the West Papua regencies, with the majority of casualties being civilians. In November, negotiations took place between the Indonesian Government and West Papuan civil society, political, and religious organizations. They agreed on a humanitarian pause in violence and the establishment of humanitarian corridors. However, the OPM was not involved in the negotiations, and rebels on the ground rejected the agreement. By 2023, the conflict had reached its deadliest recorded point, resulting in a significant number of civilian casualties. This trend was somewhat broken in 2024, as the Indonesian Government - OPM conflict intensity saw a slight decline in level of violence.
Pre-1989 Conflicts
During the Second World War, Japan conquered the so-called Netherlands Indies in present-day Indonesia. After the Japanese surrender in 1945, the Dutch moved to reclaim its colonies which led to an extra-state conflict that ended with Indonesian independence in 1949. Indonesia is an archipelago with more than 17 000 islands inhabited by a culturally diverse population, which has influenced much of the conflict history of the country. By the time of independence, the borders of the new state were unclear as the political elite in the independent country claimed some territories which had not been controlled by the Dutch, while several local leaders rejected the Indonesian concept and sought self-rule.
The expansionist policies of Indonesia became more proclaimed over time and eventually led to interstate conflict in 1962 against the Netherlands, which at the time controlled territory in the western part of the island New Guinea. Another interstate conflict took place between Indonesia and Malaysia in 1963–66. Internally, the Indonesian government was challenged by Islamic movements as well as breakaway factions from the armed forces, leading to intrastate conflict over government in 1953, and 1958–61. The country also experienced several intrastate conflicts over territory, starting in South Moluccas in 1950, and eventually followed by on-and-off fighting in West Papua in 1965–78 and in the former Portuguese colony of East Timor in 1975–89. These two conflicts then continued into the 1990s (East Timor) and 2000s (West Papua).
