Several people killed in protests against victory of incumbent President Widodo in presidential elections, which were also overshadowed by threats of terrorist attacks. After Election Commission 22 May proclaimed President Widodo winner with 55% of vote, supporters of failed candidate Prabowo Subianto, who continued to declare himself rightful winner, took to streets in protests that turned violent as police pushed them back with tear gas, rubber bullets and water cannons. Eight reported killed and hundreds injured; police reported over 250 arrests; authorities launched investigation into deaths. Chief security minister 22 May announced partial block on social media to prevent “spread of fake news”. Defence Minister Ryamizard Ryacudu warned of more riots in June as Constitutional Court hears case lodged by Subianto to annul Widodo’s victory; court scheduled to issue ruling on annulment 28 June. Govt 17 May claimed it foiled terrorist plot to detonate explosives during election results announcement; police arrested several  suspects in raids in Java early-to-mid May, believed to be members of Islamic State (ISIS)-linked Jamaah Ansharut Daulah (JAD); several reportedly returned from fighting in Syria. Police reported anti-terrorism squad had killed two suspected JAD members 4 May during raid in West Java. Violence continued in Papua province, where military reported one soldier killed in clashes with some 20 members of West Papua National Liberation Army (TPNPB) in Nduga regency 13 May.

Violence continued in Papua province, where tensions increased around national elections 17 April. Both incumbent President Widodo and his challenger, retired general Prabowo Subianto, claimed victory in presidential election; official results due 22 May, with private polls suggesting decisive lead for Widodo; Subianto continued to claim widespread fraud, raising concerns over contested result. Tensions heightened around general election in Papua’s Nduga regency as military pursued West Papua Liberation Army (WPLA); WPLA claimed it had killed two Indonesian soldiers early April, denied by military; military reported gun attack on election organisers and security forces in Alama district 18 April. WPLA claimed to have prevented voting in 32 districts, but military said voting not affected despite some exchanges of gunfire in Timika district. Two soldiers reported injured in ambush 24 April. Nduga local administration 3 April investigation report concluded that military committed human rights violations during crackdown that started in Dec 2018, and urged govt to withdraw. Report claimed almost 20,000 displaced by fighting, while Front Line Defenders NGO reported over 32,000; military said just over 3,500 displaced by armed group and rejected the report’s findings. Group of Papuan lawyers 12 April submitted judicial review to Constitutional Court challenging legality of Indonesia’s 1969 incorporation of Papua, saying that “Act of Free Choice” referendum was conducted in a way that “grossly violated the human rights of Papuans”.

Violence continued in Papua’s Nduga regency, site of Dec 2018 killing by separatist rebels of sixteen road construction workers and subsequent security operations. Military 7 March reported three soldiers and seven to ten rebels killed as estimated 70 members of “armed criminal group” with military-grade weapons as well as spears ambushed group of 25 soldiers in Nduga area; West Papua National Liberation Army reported at least five soldiers killed, accused military of burning houses and interrogating villagers, sparking violence. Military 5 March said 600 soldiers to be deployed to finish building trans-Papua highway. Thousands of villagers reportedly remain displaced. West Papua National Committee spokesperson 13 March told session of UN Human Rights Council that military was targeting indigenous Papuans and committing human rights violations; govt spokesperson blamed separatist rebels for displacements. Jamaah Ansharut Daulah (JAD) provincial leader jailed for ten years 18 March for role in May 2018 Surabaya bombings which killed 28. Ahead of 17 April presidential and legislative elections, presidential challenger Prabowo Subianto claimed massive irregularities in voter roll, raising questions over credibility of result.

Tensions continued in Papua province, while reports of terrorist activity highlighted concerns over return of foreign fighters elsewhere. In Papua, NGO Humanitarian Volunteers for Nduga 20 Feb said hundreds of students had fled fighting in Papua province’s Nduga district since Dec, although military continued to reject reports that it had fired on civilians during search for rebels suspected of Dec killing of road construction workers. Military reported that suspected separatists had opened fire on aircraft carrying military personnel and govt officials in Nduga 28 Jan, killing one soldier. Video of Papuan police threatening suspected petty thief with a snake early Feb provoked outrage; UN human rights officials 21 Feb called for independent probe into “alleged killings, unlawful arrests, and cruel, inhuman and degrading treatment of indigenous Papuans” by police and military in West Papua and Papua provinces, noting concern over “culture of impunity and general lack of investigations into allegations of human rights violations”. Police apologised, said those involved being disciplined. Police 11 Feb announced that counter-terrorist unit Densus 88 early Jan arrested man at Jakarta airport suspected of intending to travel to Syria to join Islamic State (ISIS), having previously served jail term for helping 2002 Bali bomber. Police announced that govt had sent counter-terrorist unit to Philippines, whose govt claimed that attackers in 27 Jan bomb attack in Jolo, Philippines, were Indonesian couple, although Jakarta denied (see Philippines).

Clashes continued in Papua’s central Highlands region, including regencies of Nduga, Puncak, Puncak Jaya and Lanny Jaya, as military continued pursuit of West Papua Liberation Army following early Dec killing of at least sixteen road construction workers and a soldier. Military reported at least one separatist killed in 9 Jan clash, although United Liberation Movement for West Papua said military had targeted civilians and deceased was a civilian; military also reported one soldier killed in attack in Puncak Jaya 18 Jan. United Liberation Movement for West Papua claimed six civilians have been shot dead by military. Military reportedly raided and seized offices of pro-independence West Papua National Committee (KNPB) in Timika (south) 31 Dec and charged three KNPB members with subversion. Spokesperson for office of UN High Commissioner for Human Rights Michelle Bachelet late Jan said govt has agreed in principle to grant access to Papua. Ahead of April presidential election, President Widodo was accused of trying to win over religious conservatives after govt announced radical Muslim cleric Abu Bakar Bashir, linked to 2002 Bali bombings, would be granted unconditional release; following domestic criticism and call from Australia not to show leniency, Widodo said his release would be conditional on him pledging loyalty to state and its secular ideology.

Fighting spiked day after crackdown on rallies marking anniversary of West Papuan independence with 2 Dec killing of nineteen state contractor employees working on major highway construction project in Nduga district, Papua province; West Papua National Liberation Army (TPNPB) armed group claimed responsibility, saying it regarded guards as members of military. Military launched hunt for suspects and mission to retrieve bodies; 3 Dec reported that militants using military grade weapons as well as spears and arrows attacked military post, killing one soldier and injuring two. At least four civilians reported killed in crossfire during subsequent fighting, in addition to unspecified number of soldiers and TPNPB fighters; hundreds of civilians reported to have fled to mountains. TPNPB video said group would continue armed resistance until it achieves self-determination; Coordinating Minister for Political, Legal, and Security Affairs General Wiranto dismissed idea of entering talks with group govt called “criminals”. TPNPB also called for govt to allow foreign journalists and international aid organisations to access area. Amid concern over suffering of civilians who had fled fighting, Papuan Governor Lukas Enembe 20 Dec called on President Jokowi to withdraw troops, and said local authorities would establish task force to investigate killings. Govt denied report in Australian newspaper late Dec that military had used chemical weapon white phosphorus in operation. Earlier in month, over 500 people reportedly arrested as thousands of people joined rallies in urban areas in Papua and West Papua as well as other parts of Indonesia 1 Dec marking 57th anniversary of West Papuan declaration of independence from Dutch rule; over a dozen protesters reported injured in Surabaya on Java island after clashing with nationalist paramilitary forces. UN Human Rights Office spokesperson said violence by armed groups was “unacceptable”, also that it was “troubled by the crackdown over peaceful demonstrations and increasing reports of excessive use of force by security forces, harassment, arbitrary arrests and detentions in Papua”.

Month saw further reports of clashes between military and pro-independence movement West Papua Liberation Army in Papua province’s Highlands; two Liberation Army fighters reported killed in clash with police and soldiers in Lanny Jaya district 3 Nov, after shooting dead a man they believed was spying for military. Police reportedly arbitrarily arrested over peaceful 100 pro-independence activists in Jayapura 19 Nov, releasing them next day. National Intelligence Agency reported findings that imams at dozens of mosques, including some in Jakarta attended by civil servants, were expressing support or sympathy for Islamic State (ISIS) and encouraging congregants to fight for it; also noted signs of radicalisation at university campuses.

Security forces responded harshly to peaceful protests in support of the right of self-determination in Papua prompting international criticism, while concerns over risks of new jihadist attacks remained. Govt accused Vanuatu of fuelling tensions late Sept after it voiced support for West Papuan self-determination movement at UN General Assembly and called for UN Human Rights Council to investigate rights abuses in region. UK-based TAPOL and U.S.-based East Timor and Indonesia Action Network reported authorities late Sept arrested over 120 peaceful protestors – including 39 in West Java – who voiced their support for right to self-determination; also said that at least five Papuans were tortured in Sept and one died in police custody. Military early Oct reported one Papuan killed in operation seeking members of West Papua Liberation Army in Puncak Jaya regency, Papua province; local rights activists reported two members of Liberation Army and five civilians including two children killed in land and air operations. Jakarta-based Institute for Policy Analysis of Conflict released report 18 Oct warning that Islamic State (ISIS)-linked Jamaah Ansharut Daulah, blamed for May Surabaya bombings, is still a threat and could launch attacks in west and central Java. Organisers of movement promoting moderate Islam cancelled mass rally in Yogyakarta late Oct to avoid violence after some of its supporters burned flag of outlawed Islamist group Hizb ut-Tahrir.

Authorities 4 Sept reported police shot dead two suspected militants and arrested five while seeking perpetrators of late Aug shooting of two traffic police in West Java, believed to be members of Islamic State (ISIS)-linked Jamaah Ansharut Daulah. Local media reported up to 79 people arrested after demonstrating peacefully in provincial capital Jayapura 4 Sept calling for self-determination; students protested 24 Sept supporting efforts to take West Papua issue to UN General Assembly, 67 reportedly arrested. Earthquake and tsunami that struck Sulawesi island 28 Sept killed at least 844 people, with fears death toll could reach thousands.

Court in Sumatra 21 Aug sentenced Buddhist woman to eighteen months’ jail for complaining about level of noise from her neighbourhood mosque, in controversial verdict that added to concerns that country’s strict blasphemy laws are being used to violate religious freedoms and bully minorities; moderate Islamic organisation Nahdlatul Ulama among those criticising verdict. Indonesia and Philippines 10 Aug signed agreement to enhance defence cooperation including on fighting terrorism. Police chief 7 Aug said police had arrested almost 300 terror suspects since mid-May Surabaya terror attacks. Group proclaiming itself pro-Islamic State (ISIS) hackers threatened to attack govt to avenge jailing of “brothers” and crackdown on their social media activity. Military ordered soldiers to pursue Papua National Liberation Army, suspected of killing two soldiers in ambush in Puncak Jaya regency 20 Aug.