A peaceful demonstration was carried out for three hours in Yahukimo district on Tuesday afternoon.
But friction between the people, coupled with a provocation, broke the peace as buildings were set ablaze around the demonstration area. Some participants began clashing with local police officers.
"There were victims both from the police officers and the community who were affected by police actions which resulted in death," Ahmad Musthofa Kamal, spokesperson of Papua Police, said in a written statement.
Two people died of gunshots by police officers and several people were also wounded, including a police officer.
Kamal said on Wednesday that the situation had been brought under control. He said police were planning to add more personnel to the demonstration site, partly to ensure the police there followed procedural standards.
Conflicts between Indigenous Papuans and Indonesian security forces are common in the impoverished Papua region, a former Dutch colony in the western part of New Guinea that is ethnically and culturally distinct from much of Indonesia.
Papua was incorporated into Indonesia in 1969 after a UN-sponsored ballot that was widely seen as a sham. Since then, a low-level insurgency has simmered in the mineral-rich region, which is divided into two provinces, Papua and West Papua.
In recent years, some Papua students, including some who study in other provinces, have become vocal in calling for self-determination for their region.
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