Indonesia has deployed over 1,000 security personnel to the restive province of West Papua amid spreading violent protests.
In the first of the three cities, capital of West Papua, the crowd took to the streets attacking and setting fire to some public buildings, including the Provincial Legislative Council and the former Papua Governor's Office.
Authorities are hunting for more than 250 inmates who had escaped from a prison in Sorong that was torched during the riots.
On Wednesday, about 1,000 people protested in the streets of Timika city, where demonstrators threw rocks at the local parliament building as they tried to tear down its fence.
But security personnel were not equipped with live bullets, and the situation was "generally under control", national police spokesman Muhammad Iqbal said Wednesday.
The riots were triggered by the detention of Papuan students in the city of Surabaya amid accusations of disrespect for the Indonesian flag.
The mass escape from prison occurred on Monday.
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.More news: Two American soldiers killed in Afghanistan
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Carts are set ablaze during protests in Manokwari, Papua, Indonesia, on Monday.
"Some 30 facilities in Sorong City and 13 in Manokwari are damaged", said national police chief of public information Brig.
Protesters had attacked the jail among other buildings, said Ade Kusmanto, a spokesman for the director-general of correctional facilities at the Law and Human Rights ministry.
Separate footage posted on Twitter of protests in another part of Sorong shows men in military uniform running and yelling "Get the guns, dogs!" in response to protesters throwing rocks.
Papuans say Indonesia illegally annexed the territory in the 1960s.
While a separatist movement has simmered there for decades, with frequent complaints of rights abuses by Indonesian security forces, the recent anger appears to be linked to racist slurs against Papuan students who were detained last week.
Indonesia's president Joko Widodo called for calm and the government pledged to investigate the Surabaya incident.
The employees of a state-owned contractor had been building bridges and roads as part of efforts to boost infrastructure in the impoverished region.