Indonesia: Threats and Challenges to Domestic Security

21 February 2019 Jarryd de Haan, Research Analyst, Indian Ocean Research Programme Download PDF

Key Points

  • The frequency of terrorist incidents has reached a plateau, but the growing influence of extremism will prove to be difficult to manage.
  • Separatism, especially in West Papua, could prove to be a major security hurdle in the longer term, especially if backed by international support.
  • Ethnic and religious tensions have been a significant concern in the past, but the Indonesian Government today is better equipped to deal with large-scale violence.
  • Indonesia remains a piracy hotspot and the continued complacency of local governments will make it difficult to manage.


Indonesia’s demographics, its colonial past and its sprawling archipelagic territory present the government with a unique combination of internal security challenges. This paper looks at four of those challenges and how they might affect Indonesian internal security in the future. Terrorism and extremism are two closely-related threats that the Indonesian Government must tackle carefully. Sectarian groups in key strategic provinces continue to challenge the government and may reignite separatist movements in the future. Underlying tensions in relations with some ethnic and religious groups could also threaten to erupt into violence. Finally, Indonesia’s archipelagic geography and close proximity to key global shipping routes have proven to be problematic when it comes to addressing the issue of piracy.


Terrorism and Extremism

Due to extensive media coverage, terrorism is perhaps the most well-known internal security threat facing Indonesia today. A brief spike of terrorist activity occurred in 2018, with four high-profile attacks and two failed attempts taking place between the months of May and July, resulting in 27 deaths. Of those incidents, three were attacks against police institutions and one was a co-ordinated attack against three churches in Surabaya. Overall, looking only at major terrorist incidents, 2018 saw the highest number of incidents since 2000 and the highest number of terror-related deaths since 2005.

Despite this spike in terrorist activity in 2018, there does not appear to be a rising trend in terrorist incidents. Another dataset, which includes both major and minor incidents, but excludes the 2018 data, gives the picture shown below in Figure 1. It indicates that terrorist incidents and the related deaths peaked between 1999 and 2002, and have since plateaued at a much lower level.[1] A likely explanation for the drop in terrorist incidents is the formation of Densus 88 in 2003. This is a highly specialised counter-terrorism unit formed under the control of the Indonesian National Police, in collaboration with the United States and Australia.

Terrorism in 2018 did, however, reach a new calibre. During the month of May in that year, there were three instances of suicide bombings carried out by families, including the children. One attack, on 13 May, was aimed at three separate churches. It was carried out by one family; all of the bombers – mother, father, two teenage sons and two younger daughters – died in the attacks and took twelve other casualties with them. According to Sidney Jones, a terrorism expert at the Institute for Policy Analysis of Conflict in Jakarta, those attacks marked the first time an entire family was involved, and the first time that young children (one was just eight years old), were involved in terrorist incidents in Indonesia. It does not, however, equate to a new trend in Indonesia, as all three families were closely connected to each other. That being said, it could inspire would-be attackers to include their families in possible future attacks, although that is yet to happen.

The threat of growing extremism is linked closely to terrorist attacks. While levels of extremism can be difficult to measure, extremist influences can be easily found within the public sphere. Out of one thousand mosques analysed by the Indonesian State Intelligence Agency, 4.1% preached extremist ideals and 1.7% encouraged support for Islamic State. Other reports have shown that approximately 23 per cent of high school and university students favour jihad as a method to establish an Islamic caliphate. Also, nearly 60 per cent of high school students taking extracurricular Islamic studies said that they were ready to be part of a jihad, even if violence were involved.

Countering extremist influences is difficult and it is impossible to completely eliminate those ideals from society. Two options available to the Indonesian Government are: clamping down and silencing extremist influences; and running counter-propaganda campaigns to push moderate Islamic ideals. Those options, however, are fairly limited. Silencing extremist preachers and banning extremist groups may appear to be an attractive option, but it comes with risks. Using a heavy hand on such groups could lend credibility to the view that Muslims are, in fact, being oppressed, and so, therefore, terrorism is a justifiable course of action. Counter-propaganda, on the other hand, is a cheap and low-risk approach, but its effectiveness is limited. As noted in a previous Strategic Analysis Paper, counter-propaganda efforts should be targeted at families and communities, not just men, especially given that whole families were involved in the May 2018 attacks.

Empowering moderate local clerics in mosques and pesantran schools could be an effective strategy to drown out radical voices. That being said, such campaigns can only go so far and will do little to sway those who already surround themselves with radical ideals, protected by a tightknit community of radicals. Dissuading known extremists from taking physical action is also an important step. While it may be impossible to change their beliefs, they could perhaps be persuaded to pursue the goal of jihad through non-violent means.


In its relatively short history, separatism has been a major security concern for the Indonesian Government. The separation and establishment of East Timor as an independent state in 2002 was preceded by a long and violent conflict between the occupying Indonesian army and separatist groups. Indonesia’s heavy-handed occupation of East Timor and its reluctance to relinquish control stemmed from concerns that granting independence would inspire other growing separatist groups and ultimately undermine the unity of Indonesia.

In a sense, those fears had substance. The 1999 referendum in East Timor, which resulted in the withdrawal of Indonesian forces, inspired secessionist movements in the economically strategic provinces of Aceh, Riau (which produced half of Indonesia’s oil), and Papua (then known as Irian Jaya), which held a significant share of Indonesia’s natural resources, including the world’s largest gold and copper mines, at the time. A few months after the referendum, which was held in August 1999, up to a million Acehnese gathered in the provincial capital for an independence rally – the largest single demonstration of public separatist sentiment in Indonesian history to date. Following that protest, a congress of several hundred tribal representatives met in Papua in May 2000 and declared that Indonesia’s annexation process was illegal and that the territory was legally independent. After further months of negotiation, Aceh and Papua were individually granted special autonomy laws in 2001, giving them extra powers and greater access to revenue sources within the provinces.

Today, the provinces of Aceh and Papua (now split into Papua and West Papua), remain a part of Indonesia under those special autonomy laws. While the actual threat of separatism has remained subdued since the implementation of those laws, there are growing elements calling for independence, especially within the Papuan provinces. On 25 January 2019, a petition signed by 1.8 million West Papuans[2] was delivered to the UN High Commissioner for Human Rights seeking a referendum on independence. Similar petitions, however, have been made to the UN before without success. In response to news of the most recent petition, Indonesian Minister for Defence Ryamizard Ryacudu told parliament ‘[They’re] not allowed independence. Full stop’.

While it is unlikely that the petition will succeed, the push for independence in Papua is a major internal security concern for the Indonesian Government. Growing support for independence and continuing discontent with the government risk emboldening the Free Papua Movement (Organisasi Papua Merdeka – OPM) and its military arm the West Papua Liberation Army, which could escalate attacks between those fighters and the Indonesian National Armed Forces.

Compared to Aceh, Papuan separatism may be of greater concern to the Indonesian Government because it is more likely to receive support from abroad. The independence movement in Aceh, which is over 98 per cent Muslim, receives far less international attention than the independence movement in Papua, which is 83 per cent Christian. Aceh is also known for its discriminatory policies and human rights abuses involving the application of Sharia statutes, so support for its independence will be limited simply out of concern about such policies.

Ethnic and Religious conflict

Indonesia’s relatively short history has been marred by outbursts of violence and turmoil. A well-known example is the mass killings of 1965-66, where communist sympathisers and ethnic Chinese were targeted by the Indonesian military, government and civilians. During those killings, between approximately 500,000 and one million people were killed, with some estimates reaching up to three million. The extent to which the violence was specifically directed towards Chinese Indonesians on ethnic grounds, however, is disputed, although there were hotspots of ethnic violence, especially in Sumatra. Little has been done to bring the perpetrators to justice and the Indonesian Government and military figures are reluctant to even admit that those atrocities ever took place. Many Indonesians, some of elementary school age, have also been exposed to the Suharto-era propaganda film Pengkhianatan G30S/PKI, which depicted Communists as evil, cunning and violent, and sought to justify the mass killings committed against them.

After a relatively calm period, violence began to grow again in 1996. It escalated quickly following the Asian Financial Crisis and the collapse of the Suharto Government in 1998. That time, however, the violence had more ethnic roots, with Chinese Indonesians being the primary targets during the May 1998 riots. During the riots, protesters looted and burned Chinese-owned shops with reports of owners being murdered and raped. According to Sidney Jones, the riots were triggered by various factors that caused the indigenous populace to harbour resentment against the Chinese, seeing them as a source of social vice in society and the cause of personal economic hardship. Reverberations from the 1998 riots can still be felt today in Indonesia, as ethnic tensions continue to simmer under the surface.

Both religious intolerance and ethnic tensions appear to be playing an influential role in Indonesia today. On 2 December 2016, hundreds of thousands of Muslim Indonesians gathered to protest against the Governor of Jakarta, a Chinese Christian who was accused of blasphemy. According to Greg Fealy, Associate Professor and expert in Indonesian Politics at the Australian National University, based on an examination of social media and public commentary there was a clear undercurrent of resentment towards Chinese and Christians behind the blasphemy protests.

While ethnic tensions and religious intolerance are still present, outbursts of ethnic and religious violence have since abated. The former hotspots of violence are still prone to small-scale outbursts, but they are less deadly than past large-scale violent outbreaks. Many of these small outbreaks are also related to personal grievances such as property disputes, and over places of worship. Part of the reason for this shift in the scale of violence is a more responsive security force that can intervene before violence escalates, a factor that was lacking during the May 1998 riots.

Looking at the medium-term future, in the context of internal security, ethnic tensions do not appear to present an urgent threat for the Indonesian Government. Since 2002, ethnic tensions have rarely escalated into any form of violence without other significant factors coming into play. For large-scale violence to occur, as it did in 1998, other factors such as an economic crisis will need to emerge, which seems unlikely for the medium-term future. Religious intolerance, on the other hand, appears to be attracting more attention and could present a greater concern to the Indonesian Government; although it may not be a significant threat today. Conservative Muslim groups are becoming more organised and influential and more utilised as political tools, making it easier for large protests and rallies against perceived social vices to take place. More protests and rallies could also mean more violent outbursts, as was seen in November 2016.

Piracy and Criminal Gangs

As the world’s largest archipelagic country, Indonesia’s scattered islands and heavy forests make it both a favourable location for piracy to thrive and difficult for the government to monitor. As seen in Figure 2, while global levels of piracy have fallen to their lowest level in 22 years, the number of attacks in Indonesia has moved upwards. According to the ReCAAP ISC Annual Report 2018[3], the nature of piracy attacks in Indonesia has been largely consistent in recent years with no new trends emerging. The majority of the attacks are low-level opportunistic thefts targeting tankers and bulk carriers in various Indonesian ports. There has been some concentration of attacks in the Malacca Strait and the east coast of Kalimantan, south of the Sulu Sea.

The impact of piracy on internal security is multifaceted. As well as directly threatening the lives of Indonesian civilians at sea, piracy can cause economic damage and undermine maritime security in local waters. Another particular problem caused by piracy in Indonesia, is the encouragement of corruption and fraud among local governments. Many piracy groups operate out of makeshift hidden harbours, known as pelabuhan tikus, near more remote villages or towns. In return for protection, the pirate groups will often offer funding for local schools or mosques in the village. For that reason, many local governments will turn a blind eye to those operations. When it comes to more organised, larger operations, government officials and security forces have been known to facilitate or even assist the groups in these operations in return for monetary compensation.

On another level, piracy can also be used as a means for criminal gangs and terrorist groups to obtain funds to finance their illegal activities. While the majority of low-level attacks are likely to be carried out by small local gangs that do not pose a significant threat, there have been documented cases of large-scale operations that could point towards well-organised criminal groups. Those operations have involved the perpetrators seizing control of oil tankers and taking them to another ship to siphon off the oil. They then escape with tonnes of crude oil worth hundreds of thousands of dollars; in some rare cases, potentially millions.

It is difficult to establish any strong connection between piracy and terrorist groups. Despite warnings by security analysts following the 9/11 attacks, seaborne terrorist attacks on ships have been relatively rare and often lack the widespread coverage that terrorists often seek. Terrorist groups are more likely to use piracy as a tool to obtain funds for larger attacks that would garner more coverage. That being said, there are probably simpler and more covert ways to finance such attacks and, in fact, many attacks require little or no significant funding at all.




[1] Statistics retrieved from Global Terrorism Database.

[2] The Free Papua Movement often uses the term West Papua to refer to the whole of western
New Guinea.

[3] ReCAAP ISC: Regional Co-operation Agreement on Combating Piracy and Armed Robbery against Ships in Asia – Information Sharing Centre.

Any opinions or views expressed in this paper are those of the individual author, unless stated to be those of Future Directions International.

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