Overview
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.
In 2010, 13,500 Papuan refugees lived 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.
http://www.theaustralian.com.au/news/world/protests-mar-indonesia-leader-susilo-bambang-yudhoyono-uk-visit/story-e6frg6so-1226508162585
Read more about this topic: Papua Conflict