Hundreds of police and student demonstrators clashed in the town of Manokwari.
Reports from the town say eight people were injured in protests, including four police.
A number of people are said to have received gunshot wounds.
Pro-independence demonstrations were also staged in a number of other centres.
It was the first major unrest since Indonesian police shot dead leading pro-independence figure Mako Tabuni in June, sparking a wave of violent protests.
Presenter: Liam Cochrane
Speakers: Andreas Harsono, Human Rights Watch, Indonesia.