Indonesia's Papua region was hit by fresh unrest as more than 1,000 security personnel were sent to the region after violent protests that saw buildings torched and clashes between police and demonstrators.

Indonesia's government has called for calm in its easternmost territory, where an insurgency against Indonesian rule has simmered for decades, following riots triggered by the detention of dozens of Papuan students in Java at the weekend.

About 1,000 people protested in the streets of Timika city, demonstrators were seen throwing rocks at the windows of a local parliament building as they tried to tear down its fence.

Hundreds also marched through Sorong city, and in the town of Fakfak on the western edge of the island, which is divided between Indonesia and the independent nation of Papua New Guinea.

Several cities in resource-rich Papua were brought to a standstill this week, including Manokwari where businesses and the local parliament building were set ablaze by angry demonstrators.

Authorities are hunting for more than 250 inmates who had escaped from a prison in Sorong that was torched during the riots.

Several police officers had been injured, authorities said, and there are unconfirmed reports of wounded demonstrators. No deaths have been reported.

Some 1,200 extra police and troops have been deployed to Manokwari and Sorong, according to the government and Papuan authorities.

But security personnel were not equipped with live bullets, and the situation was "generally under control", a National police spokesman said.

"It is standard that if things escalate (authorities) will deploy additional personnel," he added.

Anger boiled over at reports that authorities tear-gassed and detained 43 Papuan university students in the country's second-biggest city, Surabaya, on Saturday.

Police in riot gear stormed a dormitory to force out students who allegedly destroyed an Indonesian flag, as a group of protesters shouted racial slurs at the students.

Authorities said the students were questioned and set free.