The following is the broad timeline for major events in the Papua conflict. Notes on abbreviations: KKB = armed criminal group () KNPB = National Committee for West Papua () OPM = Free Papua Movement () TPNPB = West Papua National Liberation Army () All dates are in Eastern Indonesia Time (WIT; UTC+09:00) unless otherwise noted.
1960s to 1990s
July 1965: Raids against Indonesian soldiers and barracks in Manokwari known as Arfai incident, resulting in reprisal and suppression campaigns (Sadar Operation). In 1966 the Indonesian forces launched the major campaigns against OPM called (Bharatayudha Operations) . The operation resulted in permanently OPM expelled on Manokwari and the expulsion of OPM Battalions on Merauke and Jayapura. July–August 1969: Act of Free Choice (Indonesian: Penentuan Pendapat Rakyat, abbreviated as PEPERA) determines Western New Guinea as sovereign territory of Indonesia. June 1971: Henk de Mari reported that 55 men from two villages in North Biak were forced to dig their own graves before being shot. Published in Dutch daily De Telegraaf Oct 1974. Unknown: 500 Papuan corpses were found in jungle Lereh District, south west of Sentani Airport, Jayapura region. 1974: In North Biak, 45 Papuans were killed. 1975: In Biak, at least 41 peoples from Arwam and Rumbin villages were killed. 1976: A major operation was launched by the Indonesian Army against OPM bases in Jayapura Regency. Over 400 Indonesian soldiers and 1,600 Papuans (fighters and civilians) were reportedly killed. 1977: Aerial bombing of Akimuga (McMoRan Exploration Co. mine area). 1977–78: Aerial bombing of Baliem Valley. Apr 1978: Six unidentifiable bodies were discovered in the Dosai district of Jayapura. May 1978: Five OPM leaders surrendered to save the village they were caught in. They were beaten to death with red hot iron bars and their bodies thrown into a pit latrine. The 125 villagers were then machine gunned as suspected OPM sympathisers. June 1978: 14 corpses found shot, West of Sentani Airport, Jayapura region. 28 June 1978: Six women who were accused to have connections to the OPM were pack-raped and shot dead in Babuma. Unknown: North Biak, 12 people were shot after receiving permission to leave camp to collect sago for a village feast. 1981: 10 Papuans were killed, and 58 disappeared without trace in Paniai Region. Jun–Aug 1981: Operasi Sapu Bersih (Clean Sweep Operation); population of Ampas-Waris and Batte-Arso villages were bayoneted and left for dead. July 1984: Naval, air, and ground troop assault of Nagasawa/Ormo Kecil village; 200 were killed. Unknown: Naval shelling of Taronta, Takar, and Masi-Masi coastal villages; the survivors fled towards Jayapura; under Dutch rule in 1950 each village had a population of 1500 to 2000. 1986–87: 34 were killed in Paniai/Wissel Lake District. 31 May 1995: 11 refugees on their way to mass were shot and killed by the Indonesian Army, at the Kingmi Protestant Church near Hoya. 8 January 1996: OPM militants led by Kelly Kwalik held 26 members of the Lorentz Expedition hostage in . This triggered the Mapenduma hostage crisis (two hostages died) and the 1996 Timika shooting incident on 15 April (14–16 died). 15 May 1996: Mapenduma hostage crisis ends with the raid on OPM base in Geselama, Mimika, by Kopassus. 6 July 1998: Papuan civilians demonstrating for the independence of West Papua on the Biak Island was killed in a coordinated attack by the Indonesian military and police. Large numbers of demonstrators were detained, many unarmed civilians were tortured and killed, and their bodies dumped at sea in the massacre.
2000s
2000 6 October 2000: As police raided a flag-raising ceremony in Wamena, two non-Papuans were killed in unclear circumstances. A riot began and moved to a neighbourhood of migrants from outside of Papua, burning and looting shops. Seven Papuans were shot and twenty-four non-Papuans killed.
2001 11 November 2001: Two weeks after rejecting the autonomy law as soon as it had passed, the chairman of the Papua Presidium Council, Theys Eluay, was found murdered in his car outside Jayapura after he had been kidnapped.
2002 31 August 2002: Gunmen attacked a group of American school teachers and local employees on a sightseeing trip. Three teachers were killed, two Americans (Ricky Lynn Spier and Leon Edwin Burgon) and one Indonesian (Bambang Riwanto); and seven Americans and an Indonesian girl were wounded, including the six-year-old daughter of two of the teachers. Indonesian officials placed responsibility on the OPM; a spokesman for the group denied involvement. On 10 January 2006, Antonius Wamang, JH, MK, DM, AA, GM, JK, EO, and YD were arrested based on fingerprint evidences on all four crime scenes. Wamang was already on police watchlist being the operation commander of Kalikopi faction under Kelly Kwalik.
2003 4 April 2003 – 2003 Wamena incident: Following a raid on an Indonesian military armory which killed 2 soldiers, around 7,000 civilians were forcefully relocated and around 50 died. 5 November 2003: OPM faction leader Yustinus Murib was killed along with 9 other OPM members near Yalengga in a raid by 60 TNI personnel. SBS Dateline aired a story the day he died featuring him pleading for international intervention from a video tape received days before. 1 December 2003: A group of 500 people hoisted the separatist flag, several other actions took place, 42 people were arrested.
2004 15 January 2004: Journalist Mark Worth found dead in hotel in Sentani two days after the ABC announced his documentary, Land of the Morning Star, would premier on Australian screens in February 2004 15 October 2004: Papuan rebels killed six civilians in an attack in Puncak Jaya.
2006 13 February 2006: Formal establishment of Barisan Merah Putih which is a coalescing of earlier formed native pro-Indonesia groups. These include Indonesian Irian Youth Movement (GAPII), Red and White Movement (GMP), Council for the Determination of the Liberation of West Irian (Council for the Determination PEPERA/ DMP), People's Three Command (Trikora), West Irian Veteran Organization, and West Irian Diplomatic Veteran Group in the United Nations. 16 March 2006: Three policemen and an airman were killed and 24 other people injured during a clash with Papuan students who had been demanding closure of Freeport's Grasberg mine in Papua.
2008 9 August 2008: In Wamena, one man, Opinus Tabuni (a distant relative of Buchtar Tabuni), was killed when Indonesian security forces opened fire in response to the raising of the banned Morning Star flag by activists at a large rally organised by DAP (Dewan Adat Papua – Papuan Customary Council) marking the UN-declared International Day of the World's Indigenous People. 4 December 2008: Four Papuans were wounded by gunfire from the police at a demonstration for the independence of West Papua.
2009 29 January 2009: At least five Papuans were wounded by shots fired by police during a demonstration. 14 March 2009: One Indonesian Army soldier was killed during an attack against a security post in Tingginambut. The OPM was blamed. 8 April 2009: Several bombs exploded against a bridge and a refinery on the island of Biak. One person was killed. 11–12 April 2009: Fighting between the army and the Papuan resistance left eleven dead, including six members of the security forces. At the same time, a bomb was defused beside a police station in Biak. 15 April 2009: An attack against a convoy of police in Tingginambut killed one and wounded six. The OPM was blamed. 11 July 2009: An employee of Freeport-McMoRan Copper & Gold Inc.’s Indonesian unit was shot dead in an attack outside the company's mine in Papua. July 2009: OPM members hoisted the flag of West Papua in the village of Jugum. Afterwards more than thirty houses were burned by the Indonesian army. 16 December 2009: Free Papua Movement (OPM) leader Kelly Kwalik was shot by Indonesian police during a raid in Timika and died in Timika Hospital.
2010s
2010 24 January 2010: Rebels ambushed a convoy of mining company PT Freeport McMoRan employees. Nine people were injured; OPM denied responsibility. 1 March 2010: The Australian West Papua Association in Sydney said that the situation in West Papua was deteriorating. Since the previous July there had been fourteen incidents of shootings around the Grasberg mine, Freeport's copper and gold mine. The attacks had killed at least three and injured thirteen. 23 March 2010: Rebels attacked an Indonesian military convoy, injuring some of the soldiers. May 2010 : The OPM were suspected of killing three workers at a construction site. In retaliation the Indonesian military raided a village leaving at least two dead and a woman raped, while houses in three villages were burned by the military. 17 May 2010: The army attacked a base of OPM killing one suspected militant. 21 May 2010: Militants attacked members of the Indonesian army near Yambi, 75 km from Mulia. No casualties were reported. 15 June 2010: An officer of the Indonesian elite police was shot dead during a patrol. Eight firearms were also stolen by the rebels. July 2010: Twelve houses and two churches were destroyed and a woman was raped during an Indonesian army operation to capture Goliath Tabuni.
2011 23 June 2011: A police officer from Jayapura was shot by alleged members of the Free Papua Movement. 6 July 2011: Three soldiers were shot during a clash with unknown attackers in Kalome village, Tingginambut district. 20 July 2011: An Indonesian soldier was killed in an ambush targeting a military security squad in Puncak Jaya district in Papua. 31 July 2011: Rebels attacked a car in Papua with guns, axes and knives killing one soldier and three civilians and also wounding seven; OPM denied responsibility. 1 August 2011: The National Police said that members of the Free Papua Movement killed four civilians near Tanjakan Gunung Merah, Paniai. 2 August 2011: A soldier guarding a military post in Tingginambut was shot dead. In the town of Mulia two shootings targeted the police and military, injuring one soldier. 3 August 2011: Separatists shot at an army helicopter as it evacuated the body of a soldier they had allegedly killed. 22 October 2011: Al Jazeera published footage of an independence gathering that was attacked by Indonesian security forces. At least five people were killed. 2 December 2011: An officer from Jayapura Police office was found dead next to a river after he was allegedly slain by a group wielding arrows and daggers. OPM was blamed. 5 December 2011: Two policemen were killed in Puncak Jaya during an exchange of gunfire with suspected members of the Free Papua Movement. 12 December 2011: Police attacked the headquarters of a local cell of the OPM. The police seized firearms, ammunition, knives, combat gear, documents, and Morning Star flags, and killed 14 militants.
2012 In 2012, West Papuan National Committee's (KNPB) Chairman Mako Tabuni died in hospital after sustaining a shooting injury during an arrest attempt by the Jayapura police department.
2013 22 February 2013: A military helicopter was damaged by ground fire while attempting to remove the bodies of soldiers killed fighting the OPM earlier. At least three members of the crew were injured. Eight Indonesian soldiers were killed in fighting around the same time. 26 December 2013: Gerald Little (an Australian) was sentenced to seven months in prison in Australia for attempting to fight with the OPM. Little was arrested in December 2012 at Brisbane airport by police. Little who had no military training, combat experience or espionage training at the time travelled to Ukraine in August 2012 for a five-day training course run by a private military contractor, the International Bodyguard Association (IBA). The Judge described Little as delusional. Little had been in email communication with the OPM.