The source of the human rights problems in West Papua is the colonization and subsequent dispossession of the lands and resources of the indigenous peoples. They have been prevented from exercising their fundamental freedoms, including their right to development in accordance with their own needs and interests.

A frequent and pervasive cause of dispute has been over land rights. The appropriation of tribal or clan land for development projects, from forestry, mining or road construction to Transmigration settlements, has resulted in large numbers of indigenous people being removed from their traditional land, invariably leading to conflict with the armed forces as well as physical and emotional harm for the people affected. Since the takeover of West Papua by Indonesia in 1963, violations of human rights have been widespread. Many of the violations have occurred in the context of on-going conflict between the OPM (Organisasi Papua Merdeka, or Free Papua Movement) and the Indonesian forces.

Since the takeover there has been a popular peaceful resistance, supported across the province. According to Amnesty International’s 1994 report, there are over 140 political prisoners from West Papua currently serving sentences of between two years and life imprisonment for subversion. Many of these are prisoners of conscience, jailed for their non-violent political activities or beliefs.

During the 1960s and mid 1970s, a number of rebellions took place in Manokwari, Enarotali and other regions including the Baliem Valley. The Freeport mining installations were attacked by the OPM with the local Amungme people in 1977. The army exacted a heavy toll in response to these attacks, bombing and strafing villages and killing thousands of civilians. As ABRI (Indonesian armed forces) troops were incapable of penetrating the jungle to discover guerrilla camps, they resorted to reprisals. To stamp out armed resistance, villages were attacked and suspected subversives were summarily executed. Others were forcibly resettled in low altitudes, where twenty per cent of infants died because of lack of resistance to malaria.

The army also conducted operations to undermine support for the resistance by persecuting the families of people believed to be fighting in the bush. The wives of guerrillas were assaulted, their parents arrested. Villages suspected of supporting the OPM were destroyed, people chased from their homes, livestock killed and property looted. It is difficult to put an exact figure on the number of West Papuans killed since Indonesia took control in 1963, but estimates vary from between 70,000 to 200,000.