The Jakarta administration has had a policy of facilitating the official settlement of Indonesians from densely populated areas of Indonesia such as Java to West Papua and other places, particularly to the east of the archipelago. Transmigration threatens indigenous survival, causing the political seizure of indigenous land. The settlement of hundreds of thousands of Indonesians in West Papua has had no impact on population pressures in Java and elsewhere; yet hundreds of thousands of people are placing unsustainable pressures on indigenous communities and cultures. The key underlying political rationale for the settlement of outsiders is a geo-strategic one: to control and box-in the native population - at the Papua New Guinea border in particular - and to ensure Papuans are dispersed, surrounded by settlers. Transmigrant settlements typically have 75% newcomers, and 25% native Papuans.

Transmigration, both official and spontaneous, provides Indonesian labour for the resource extraction companies, but inevitably brings a military presence, and further pressure on indigenous communities. West Papuans also fear they may one day become a minority in their own land.