At least 200 demonstrators forced their way into a legislative building in Indonesia's Papua province on Monday.
According to witnesses, the crowd was calling for the withdrawal of Indonesian troops from the region.
Calm was restored by nightfall, the Associated Press said, after a meeting with legislators.
The incident came amid high tension following the shooting of a student last week during clashes in the central Papua district of Paniai.
The protesters were shouting "Indonesian troops get out of West Papua" as they stormed the building, witnesses told the Associated Press.
West Papua is usually the term used by independence activists to refer to the province.
On Friday, two people were injured and one person killed during clashes outside a police station.
It was not clear why that unrest erupted. According to the Indonesian news agency Antara, violence broke out after three people were told to stop taking monetary donations from residents while repairing roads in the area.
But Australian shadow foreign affairs spokesman Kevin Rudd has said he is concerned the violence is a reprisal by the authorities for a row over 43 Papuans who have recently sought asylum in Australia.
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