The Papua conflict is an ongoing low-level conflict between the Indonesian Government and portions of the indigenous populations of West Papua in the Indonesian provinces of Papua and West Papua on the island of New Guinea. Since the withdrawal of the Dutch colonial administration from the Netherlands New Guinea in 1962, the implementation of Indonesian governance in 1963 and the formal absorption of West Papua into Indonesia in 1969, the Free Papua Movement (OPM), a militant Papuan-independence organization, has conducted a low-level guerrilla war against the Indonesian state, targeting the Indonesian military and police, as well as engaging in the kidnapping of both non-Papuan Indonesian settlers and foreigners. West Papuans have conducted various protests and flag-raising ceremonies for independence or federation with Papua New Guinea, and accuse the Indonesian government of indiscriminate violence and of suppressing their freedom of expression. Many West Papuans have been killed by the Indonesian military since 1969 and the Indonesian governance style has been compared to that of a police state, suppressing freedom of political association and political expression. The Indonesian Government restricts foreign access to the Papua and West Papua provinces due to sensitivities regarding its suppression of Papuan nationalism.
In December 1949, at the end of the Indonesian National Revolution, the Netherlands agreed to recognize Indonesian sovereignty over the territories of the former Dutch East Indies, with the exception of Western New Guinea, which the Dutch continued to hold as Netherlands New Guinea. The nationalist Indonesian government argued that it was the successor state to the whole of the Dutch East Indies and wanted to end the Dutch colonial presence in the archipelago. The Netherlands argued that the Papuans were ethnically different and that the Netherlands would continue to administer the territory until it was capable of self-determination. From 1950 on the Dutch and the Western powers agreed that the Papuans should be given an independent state, but due to global considerations, mainly the Kennedy administration's concern to keep Indonesia on their side of the Cold War, the United States pressured the Dutch to sacrifice Papua's independence and transfer the country to Indonesia.
In 1962, the Dutch agreed to relinquish the territory to temporary United Nations administration, signing the so-called New York Agreement, which included a provision that a plebiscite would be held before 1969. The Indonesian military organised this vote, called the Act of Free Choice in 1969 to determine the population's views on Papua and West Papua's future; the result was in favor of integration into Indonesia. In violation of the Agreement between Indonesia and the Netherlands, the vote was a show of hands in the presence of the Indonesian military, and only involved 1025 hand picked people who were forced at gunpoint to vote for integration with Indonesia, much less than 1% of those who should have been eligible to vote. The legitimacy of the vote is hence disputed by independence activists, who launched a campaign of protests against the military occupation of West Papua by Indonesia.
The Indonesian government is accused of human rights abuses, such as attacks on OPM-sympathetic civilians and jailing people who raise the West Papuan National Morning Star flag for treason. Official estimates are that up to 450,000 Indigenous Papuans have been killed in the conflict. (Such numbers amount to Genocide under UN Constitution).
Through the transmigration program, which since 1969 includes migration to Papua, about half of the 2.4 million inhabitants of Indonesian Papua are born in Java, though intermarriage is increasing and the offspring of transmigrants have come to see themselves as "Papuan" over their parents' ethnic group.
As of 2010, 13,500 Papuan refugees live in exile in the neighboring independent state of Papua New Guinea (PNG), and occasionally the fighting spills over the border. As a result, the Papua New Guinea Defence Force has set up patrols along PNG's western border to prevent infiltration by the OPM. Additionally, the PNG government has been expelling resident "border crossers" and making a pledge of no anti-Indonesian activity a condition for migrants' stay in PNG. Since the late 1970s, the OPM have made retaliatory "threats against PNG business projects and politicians for the PNGDF's operations against the OPM". The PNGDF has performed joint border patrols with Indonesia since the 1980s, although the PNGDF's operations against the OPM are "parallel".
In 2004, the UK based Free West Papua Campaign was set up by exiled West Papuan leader Benny Wenda to encourage the UN to hold an Independence Referendum in West Papua. The Campaign has growing International support and the backing of notable figures such as Nobel Peace Laureate Archbishop Desmond Tutu. In 2012, the Campaign issued an arrest warrant for Indonesian President Susilo Bambang Yudhoyono for his state visit to the UK in October–November that year. Yudhoyono was protested against everywhere he went in London and regularly saw West Papuan National Flags of Independence which are illegal in Indonesia
Brief summary and outline of major events
United Nations Administration (1 October 1962– 30 April 1963)
Main article: United Nations Temporary Executive Authority
- August 15, 1962: New York Agreement by Kingdom of the Netherlands, Republic of Indonesia and United Nations. Region of West Papua submitted by Netherlands to UN temporary authority, which transferred governance to Indonesia on 1 May 1963. Implementation of Indonesian governance was followed by sporadic fighting between Indonesian and pro-Papuan forces until 1969.
New Order 1965-1998
- 1966–67: Aerial bombing of Arfak Mountains.
- Jan–Mar 1967: Aerial bombing of Ayamaru and Teminabuan areas.
- 1967: Operasi Tumpas (operation obliteration). 1,500 alleged dead in Ayamaru, Teminabuan and Inanuatan.
- Apr 1969: Aerial bombing of Wissel Lake District (Paniai and Enarotali area); 14,000 survivors escape into the jungle.
- July–August 1969: Act of Free Choice / PEPERA determines West Papua Region as sovereign territory of Republic 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 people from Arwam and Rumbin villages were killed.
- 1977: Aerial bombing of Akimuga (Freeport McMoRan Inc. 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 (Organisasi Papua Merdeka) leaders surrendered to save the village they were caught in. They are 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 sympathizers.
- June 1978: 14 corpses found shot, West of Sentani Airport, Jayapura region.
- 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. Paniai Region.
- Jun–Aug 1981: Operasi Sapu Bersih (Operation Clean Sweep), populations of Ampas-Waris and Batte-Arso villages were bayoneted and left for dead.
- Sep–Dec 1981: An estimated 13,000 Papuans were killed in the central highlands.
- 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.
- 24 June 1985: 2,500 were killed in Paniai area of Wissel Lake district, including 115 from Iwandoga and Kugapa villages.
- 1986–87: 34 were killed in Paniai/Wissel Lake District.
- 8 January 1996: OPM militants led by Kelly Kwalik held 26 members of Lorentz Expedition as hostage in Mapenduma. Triggering Mapenduma hostage crisis (2 hostages died) and 1996 Timika shooting incident on 15 April (16 died).
- 9 May 1996: Mapenduma hostage crisis ends with the raid on OPM base in Geselama, Mimika, by Kopassus.
- October 6, 2000: As police raid a flag-raising ceremony in Wamena, a mob formed and two non-Papuans were killed in unclear circumstances. The mob started to riot and moved to a neighborhood of migrants from other parts in Indonesia, while also burning and looting shops. Seven Papuans are shot and twenty-four non-Papuans are killed.
- November 11, 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.
- August 31, 2002: Gunmen attacked a group of American school teachers and local employees on a sightseeing trip. Two Americans and one Indonesian were killed, and seven Americans and an Indonesian girl were wounded. Indonesian officials placed responsibility on the OPM; a spokesman for the rebel group denied involvement. 
- December 1, 2003: A group of 500 people hoisted the separatist flag, several other actions took place, 42 people were arrested.
- October 15, 2004: Papuan rebels killed six civilians in an attack in Puncak Jaya.
- March 16, 2006: Three policemen and an airman were killed and 24 other people injured during a clash with papuan and students who have been demanding closure of Freeport's Grasberg mine in Papua.
- August 9, 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 organized by DAP (Dewan Adat Papua – Papuan Customary Council) marking the UN-declared International Day of the World's Indigenous People.
- December 4, 2008: 4 Papuans were wounded by gunfire from the police at a demonstration for the independence of West Papua.
- January 29, 2009: At least 5 Papuans were wounded by shots fired by police during a demonstration.
- March 14, 2009: One Indonesian Army soldier was killed during an attack against a security post in Tingginambut. The OPM was blamed.
- April 8, 2009: Several bombs exploded against a bridge and a refinery on the island of Biak. One person is killed.
- April 9, 2009: A bomb attack in Jayapura killed 5 and severely injured several others. Meanwhile, about 500 militants attacked a police post with bows and arrows and petrol bombs. One died after shot by police in the incident.
- April 11–12, 2009: Fighting between the army and the Papuan resistance left 11 dead including 6 members of the security forces. At the same time, a bomb was defused against a police station in Biak.
- April 15, 2009: An attack against a convoy of police in Tingginambut killed one and wounded six. The OPM is blamed.
- July 11, 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 30 houses were burned by the Indonesian army.
- August 12, 2009: A convoy of 16 buses for employees of Freeport-McMoRan Copper's was ambushed. Two people were killed and 5 wounded.
- December 16, 2009: Free Papua Movement (OPM) leader Kelly Kwalik was shot by Indonesian police during a raid in Timika and died in Timika Hospital.
- January 24, 2010: Rebels ambushed a convoy of mining company PT Freeport McMoran employess. Nine people were injured, OPM denied responsibility.
- March 1, 2010: The Australian West Papua Association in Sydney said that the situation in West Papua is deteriorating. Since last July there have been 14 incidents of shootings around the Grasberg mine, Freeport's copper and gold mine, these attacks had killed at least 3 and injured 13.
- March 23, 2010: Rebels attacked an Indonesian military convoy, Injuring some of the soldiers in the convoy.
- May, 2010 : The OPM were suspected of killing 3 workers at a construction site, In retaliation the Indonesian military raided a village leaving at least 2 dead and a woman raped while houses in 3 villages were burned by the military.
- May 17, 2010: The army attacked a base of OPM killing one suspected militant.
- May 21, 2010: Militants attacked members of the Indonesian army near Yambi, 75 km from Mulia. No casualties were reported.
- June 15, 2010: An officer of the Indonesian elite police was shot dead during a patrol, Eight firearms were also stolen by the rebels.
- July, 2010: 12 houses and two churches were destroyed and a woman was raped during an Indonesian army operation to capture Goliath Tabuni.
- June 23, 2011: A police officer from Jayapura, was shot by alleged members of the Free Papua Movement.
- July 6, 2011: Three soldiers were shot during a clash with unknown attackers in Kalome village, Tingginambut district.
- July 20, 2011: An Indonesian soldier was killed in an ambush against a military security squad in Puncak Jaya district in Papua.
- July 31, 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.
- August 1, 2011: The National Police said that members of the Free Papua Movement killed four civilians near Tanjakan Gunung Merah, Paniai.
- August 2, 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.
- August 3, 2011: Separatists shot at an army helicopter as it evacuated the body of a soldier they had allegedly killed.
- October 22, 2011: Al Jazeera published footage of an independence gathering that was attacked by Indonesian security forces. At least five people were killed.
- December 2, 2011: An officer from Jayapura Police office was found dead next to a river on Thursday after he was allegedly slain by a group wielding arrows and daggers. OPM was blamed.
- December 5, 2011: Two policemen were killed in Puncak Jaya during an exchange of gunfire with suspected members of the Free Papua Movement.
- December 12, 2011: police attacked the headquarters of a local cell of the OPM. The police seized firearms, ammunition, knives, combat gear, documents, Morning Star flags and killed 14 militants.
- In 2012, West Papuan National Committee's (KNPB) Chairman Mako Tabuni died in hospital after sustained shooting injury during an arrest attempt by Jayapura police department.
- February 22, 2013, a military helicopter was damaged by ground fire while attempting to remove the bodies of soldiers killed fighting the OPM earlier. At least 3 members of the crew were injured. 8 Indonesian army soldiers were killed in fighting around the same time.
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