The failed coup released pent-up communal hatreds which were fanned by the army who quickly blamed the Indonesian Communist Party (PKI). Communists were purged from political, social, and military life, and the PKI itself was banned. The massacres began in October 1965 in the weeks following the coup attempt, and reached their peak over the remainder of the year before subsiding in the early months of 1966. They started in the capital Jakarta, spread to Central and East Java, and later Bali. Thousands of local vigilantes and army units killed actual and suspected PKI members. Although killings occurred across Indonesia, the worst were in PKI strongholds of Central Java, East Java, Bali, and northern Sumatra. It is possible that over 1 million people were imprisoned at one time or another.
On the evening of 30 September and 1 October 1965, six generals were killed by a group calling themselves the 30 September Movement. With much of Indonesia's top military leaders either dead or missing, one of the most senior surviving generals, Suharto (later Indonesian President) assumed control of the army the following morning. By 2 October he was firmly in control of the capital and announced that a coup attempt had failed. The military blamed the coup attempt on their arch enemies the PKI.On 5 October, the day of the dead generals' funeral procession, a military propaganda campaign began to sweep the country, successfully convincing both Indonesian and international audiences that it was a Communist coup, and that the murders were cowardly atrocities committed against Indonesian heroes. The PKI's denials of involvement had little effect. Pent-up tensions and hatreds that had built up over years were released.
The communal tensions and hatreds built up were played upon by the army leadership who demonised communists, and many ordinary Indonesians became killers. The worst massacres were in Central and East Java where PKI support was at its strongest. Large numbers of victims were also reported in northern Sumatra and Bali. The situation varied across the country and the role of the army has never been fully explained; in some areas the army organised, encouraged, trained, and supplied civilian to groups and local militias. In other areas, communal vigilante action preceded the army, although in most cases killings did not commence before military units had sanctioned violence by instruction or example. In some areas, civilian militia knew where to find known communists and sympathisers, while in others, the army demanded lists of communists from village heads. PKI membership was not disguised and most suspects were easily identified within communities. The American Embassy in Jakarta, supplied the Indonesian military with lists of up to 5,000 suspected communists.
Although some PKI branches organised resistance and reprisal killings, most went passively to their deaths. Not all victims were PKI members; often the label "PKI" was used to include anyone to the left of the Indonesian National Party, in other cases victims were suspected or simply alleged Communists. Local Chinese were killed in some areas, and their properties looted and burned as a result of anti-Chinese racism on the excuse that Aidit had brought the PKI closer to China. In the predominantly Christan islands of Nusa Tenggara, Christian clergy and teachers suffered at the hands of Muslim youth. In West Kalimantan, approximately eighteen months after the worst of the killings in Java, indigenous Dayaks expelled 45,000 ethnic Chinese out of rural areas, in which hundreds, or perhaps thousands were killed. Methods of killing included gun shot and beheading with Japanese-style Samurai swords. Corpses were often thrown into rivers and at one point, officials complained to the army that the rivers running into the city of Surabaya were clogged with bodies. In areas such as Kediri in East Java, Nahdlatul Ulama youth wing (Ansor) members lined up Communists, cut their throats and disposed of the bodies in rivers. The killings left whole sections of villages empty, the houses of victims or the interned were looted and often handed over to the military.
Although there were occasional and isolated flare ups until 1969, the killings largely ended by March 1966, until either there were no more suspects, or authorities intervened. Many of the bodies had been dumped in rivers, so much so that in parts they became clogged with corpses. Solo residents said that exceptionally high flooding of the mystical Solo River in March 1966 signaled the end of the killings.
Conflict that had broken out in 1963 between Muslim party Nahdlatul Ulama (NU) and the PKI became slaughter in the second week of October Muslim group, Muhammadiyah proclaimed in early November 1965 that the extermination of "Gestapu/PKI" constituted Holy War ("Gestapu" being the military's name for the '30 September Movement'), a position that was supported by other Islamic groups in Java and Sumatra. For many youths, killing Communists became a religious duty. Roman Catholic students in the Yogyakarta region, would leave their hostels at night to join in the execution of truckloads of arrested communists.
In mid-October, Suharto sent in paracommando troops he trusted as loyal into Central Java, a region with strong communist allegiances, while troops of whose loyalty he was suspicious, were ordered out. Anti-communist killings were then instigated with youths assisted by the army to find Communists.
Where there had been communist centres in Central and East Java, Muslim groups portraying themselves as victims of communist aggression justified the killings by evoking the Madiun Affair of 1948.
Although, for most of the country, the killings subsided in the first months of 1966, in parts of East Java, the killings went on for years. In Blitar, guerrilla action was maintained by surviving PKI members until they were defeated in 1967 and 1968. A mystical teacher, Mbah Suro, and his devotees of his Communist ideas mixed with traditional mysticism built an army, but Suro and eighty of his followers were killed in a war of resistance against the army.
Like parts of East Java, Bali experienced a state of near civil war as Communists regrouped. The balance of power was shifted in favour of anti-Communists in December 1965, when the Army Paracommando Regiment and Brawijaya units arrived in Bali after having carried out killings in Java. Javanese military commanders permitted Balinese squads to kill until reined in. In contrast to Central Java where the army encouraged people to kill the "Gestapu", on Bali eagerness to kill was so great and spontaneous, that having provided logistic support, the army had to step in to prevent anarchy. A series of killings similar to those in Central and East Java were led by black-shirted PNI youth. For several months, militia death squads went through villages capturing suspects and taking them away. Between December 1965 and early 1966, an estimated 80,000 Balinese were killed, equivalent to 5% of the island's population at the time, and proportionally more than anywhere else in Indonesia.
In the first 20 years following the killings, thirty-nine serious estimates of the death toll were attempted. Before the killings had finished, the army estimated 78,500 had died while another early estimate by the traumatised Communists put the figure at 2 million. The army later estimated the number killed at a possibly exaggerated 1 million. In 1966, Benedict Anderson estimated the deaths at 200,000 and by 1985 had offered a range of 500,000 to 1 million. Most scholars agree that at least half a million were killed, more than any other event in Indonesian history. An armed forces security command estimate from December 1976 put the number at between 450,000 and 500,000.
Arrests and imprisonment continued for 10 years after the purge. A 1977 Amnesty International report suggested "about one million" PKI cadres and others identified or suspected of party involvement were detained. Between 1981 and 1990, the Indonesian Government estimated that there were between 1.6 and 1.8 million former prisoners "at large" in society. It is possible that in the mid 1970s, 100,000 were still imprisoned without trial. It is thought that as many as 1.5m were imprisoned at one stage or another. Those PKI members not killed or imprisoned went into hiding while others tried to hide their past. Those arrested included leading politicians, artists and writers such as Pramoedya, and peasants and soldiers. Many did not survive this first period of detention, dying from malnutrition and beatings. As people revealed the names of underground Communists, often at the hands of torture, the numbers imprisoned rose from 1966–68. As many as 1.5 million may have been imprisoned. Those released were often placed under house arrest, had to regularly report to the military, or were banned from Government employment, as did their children.
The killings are skipped over in most Indonesian histories, and have received little introspection by Indonesians and comparatively little international attention. However, following Suharto's forced resignation in 1998, and his death in 2008, some level of openess about what had really happened has emerged in public discourse in subsequent years. A hesitant search for mass graves by survivors and family members began after 1998, although little has been found. Over three decades later, great enmity remains in Indonesian society over the events. The film Year of Living Dangerously based on events surrounding the killings was not able to be shown in Indonesia until 1999.
Satisfactory explanations for the scale and frenzy of the violence have challenged scholars from all idealogical perspectives. One view attributes the communal hatreds behind the killings to the forcing of parliamentary democracy onto Indonesian society, claiming that such changes were culturally unsuitable and unnecessarily disruptive in the post-independence 1950s. A contrasting view is that when Sukarno and the military replaced the democratic process with authoritarianism, competing interests—i.e., the army, political Islam, and Communism—could not be openly debated, rather they were suppressed and could only be expressed through violence. Conflict resolution methods have broken down, and Muslim groups and the military adopted an "us or them attitude", and that when the killings were over, many Indonesians dismissed as something the communists had deserved. The possibility of a return to similar upheavals is cited as a factor in the "New Order" administrations political conservatism and tight control of the political system. Vigilance against a Communist threat remained a hallmark of Suharto's thirty-year presidency. Internationally, the killings and purges were seen as a victory over Communism at the height of the Cold War. Western governments and much of the West's media preferred Suharto and the "New Order" to the PKI to the increasingly leftist "Old Order".