[also called West Irian War]

A connection between the Sukarno and Suharto eras was the ambition to build a unitary state whose territories would extend "from Sabang [an island northwest of Sumatra, also known as Pulau We] to Merauke [a town in southeastern Irian Jaya]." Although territorial claims against Malaysia were dropped in 1966, the western half of the island of New Guinea and East Timor, formerly Portuguese Timor, were incorporated into the republic. This expansion, however, stirred international criticism, particularly from Australia.

West New Guinea, as Irian Jaya was then known, had been brought under Indonesian administration on May 1, 1963 following a ceasefive between Indonesian and Dutch forces and a seven-months UN administration of the former Dutch colony. A plebiscite to determine the final political status of the territory was promised by 1969. But local resistance to Indonesian rule, in part the result of abuses by government officials, led to the organization of the Free Papua Movement (OPM) headed by local leaders and prominent exiles such as Nicholas Jouwe, a Papuan who had been vice chairman of the Dutch-sponsored New Guinea Council. Indonesian forces carried out pacification of local areas, especially in the central highland region where resistance was particularly stubborn.

Although Sukarno had asserted that a plebiscite was unnecessary, acceding to international pressure, he agreed to hold it. The Act of Free Choice provisions, however, had not defined precisely how a plebiscite would be implemented. Rather than working from the principle of one man-one vote, Indonesian authorities initiated a consensus-building process that supposedly was more in conformity with local traditions. During the summer of 1969, local councils were strongly pressured to approve unanimously incorporation into Indonesia. The UN General Assembly approved the outcome of the plebiscite in November, and West Irian (or Irian Barat), renamed Irian Jaya, became Indonesia's twenty-sixth province. But resistance to Indonesian rule by the OPM, which advocated the unification of Irian Jaya and the neighboring state of Papua New Guinea, continued. Border incidents were frequent as small bands of OPM guerrillas sought sanctuary on Papua New Guinea territory.