U.S. officials understood at the outset that Indonesia would never allow West Irian to become independent and that it was unlikely to ever allow a meaningful act of self-determination to take place. The Johnson and Nixon administrations were equally reluctant to challenge Indonesian control over West Irian, especially after the conservative anti-Communist regime of General Suharto took over in 1966 following
an abortive coup attempt which led to the slaughter of an estimated 500,000 alleged Communists. Suharto quickly moved to liberalize the Indonesian economy and open it to the West, passing a new foreign investment law in late 1967. The first company to take advantage of the law was the American mining company Freeport Sulphur, which gained concessions to vast tracts of land in West Irian containing gold and copper reserves. (Note 2)
Over six weeks from July to August 1969, U.N. officials conducted the so-called "Act of Free Choice." Under the articles of the New York Agreement (Article 18) all adult Papuans had the right to participate in an act of self-determination to be carried out in accordance with international practice. Instead, Indonesian authorities selected 1022 West Papuans to vote publicly and unanimously in favor of integration with Indonesia.
http://www.gwu.edu/~nsarchiv/NSAEBB/NSAEBB128/index.htm