As many as 1,200 police personnel were being dispatched to eastern Indonesia's West Papua province as a fresh protest became a riot on Wednesday.
Protests sparked by accusations that security forces had arrested and insulted Papuan students in East Java's Surabaya city turned violent on Monday, when demonstrators torched a local legislative building and set fire to cars in Manokwari, the provincial capital.
Indonesian authorities are hunting for more than 250 inmates who escaped from a prison in the province of West Papua.
About 1,000 people protested in the streets of Timika city, throwing rocks at the local parliament building as they tried to tear down its fence.
Indonesian national police spokesman Dedi Prasetyo told the ABC that 960 additional police officers from provinces around the country had been sent to the region to "clean up".
The students were taken to a police headquarters after being accused of disrespecting the Indonesian flag in front of their dormitory during an Independence Day ceremony.
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The prison break happened Monday as several cities in Indonesia's easternmost territory - where an insurgency against Jakarta's rule has simmered for decades - saw rioting and protests triggered by the detention of dozens of Papuan students.
The governor said that she had personally called Papua Governor Lukas Enembe to extend her apology for the ill treatment of Papuan students in East Java, which led thousands of Papuans to take to the streets.
The crowd began to disperse as riot police fired warning shots in the air.
Internet speeds in the area had also been slowed as part of the efforts to prevent hoaxes spreading, a spokesman at the information and communication ministry said.
Papua and West Papua provinces, the resource-rich western part of the island of New Guinea, were a Dutch colony that was incorporated into Indonesia after a widely criticised UN-backed referendum in 1969.
Indonesia's police headquarter said it sent 15 teams of police from Sulawesi, Bali, and Maluku after riots erupted in Manokwari town, Sorong city and Fakfak Regency of West Papua. The protesters demanded that the government and other Indonesian citizens outside the region put an end to racial abuse against Papuans.