At least 20 people were killed and dozens more injured as fresh unrest erupted in Indonesia's restive Papua region Monday, with some victims burned to death in buildings set ablaze by protesters, authorities said.

"Most of them died in a fire," said Papua military spokesman Eko Daryanto.

"The death toll could go up because many were trapped in burning kiosks," he added.

Papua, on the western half of New Guinea island, has been gripped by weeks of violent protests fuelled by anger over racism, as well as fresh calls for self-rule in the impoverished territory.

On Monday, 16 people died in Wamena city where hundreds demonstrated and burned down a government office and other buildings earlier in the day, authorities said.

Among the victims, 13 were non-Papuans and three were Papuans, Daryanto said, adding that a soldier and three civilians also died in provincial capital Jayapura, where security forces and stone-throwing protesters clashed Monday.

The soldier was stabbed to death, the military said.

It was not immediately clear how the civilians in Jayapura died.

About 300 people were arrested in connection with Monday's protests, Daryanto said, adding that about 65 people had been injured.

The clashes in Papua had quietened down in recent days, but flared up again as hundreds took to the streets — and houses and stores went up in flames.

Monday's protests in Wamena — mostly involving high-schoolers — were reportedly sparked by racist comments made by a teacher, but police have disputed that account as a "hoax".

Indonesia routinely blames separatists for violence in Papua, its easternmost territory, and conflicting accounts are common.

Demonstrations broke out across the region and in other parts of the Southeast Asian archipelago after the mid-August arrest and tear-gassing of dozens of Papuan students, who were also racially abused, in Indonesia's second-biggest city, Surabaya.

A low-level separatist insurgency has simmered for decades in Papua, a former Dutch colony, after Jakarta took over the mineral-rich region in the 1960s. A vote to stay within the archipelago was widely viewed as rigged.

Earlier Monday, authorities said the situation had been brought under control in Wamena, while an AFP reporter there said Internet service had been cut.

"Security forces have also taken steps to prevent the riots from spreading," said National Police spokesman Dedi Prasetyo.

The airport in Wamena was shut Monday with some 20 flights canceled due to the unrest, local media reported, citing an airport official.

Indonesia has sent thousands of security personnel to Papua to quell the recent unrest, and dozens were arrested for instigating the earlier riots.

At least five demonstrators and a soldier were killed, but activists say the civilian death toll is higher.

Last week the military said a toddler and teenager were among three people killed in a gunfight between security forces and independence-seeking rebels.