Indonesian security forces have opened fire on Papuan protesters, killing six people who tried to storm a government office in Deiyai region, a local resident and a website citing a separatist group said.

Many were injured in the clash in Indonesia's easternmost province, Deiyai resident John Pakage told Reuters by telephone.

The website giving the same toll is Suarapapua.com.

AAP

In Jakarta, national police spokesman Dedi Prasetyo dismissed reports of protesters being killed as "a provocation", but said one military personnel was killed and three police officers injured in a clash.

"Security forces are trying to control the security in the area," he said.

A Papuan news portal, jubi.com, said thousands of people, some carrying bows and arrows, were protesting in Deiyai.

Mr Prasetyo of the police said only information from the Papua police was trustworthy.

READ MORE Thousands take to streets as Papua protests continue

"We don't know yet how many victims because communication from there has been limited," Papuan military spokesman Eko Daryanto told Reuters by phone.

Yones Douw, a senior official with a Papuan church organisation based in a region near Deiyai, told Reuters the situation remained "tense" after protesters clashed with security forces outside a local government office around 2 pm local time.

In Jakarta, dozens of students protested near the presidential palace, local media reported. Photos showed that some protesters had painted on their face the symbol from a banned flag of a Papuan independence movement.

Thousands of Papuans have been protesting over perceived ethnic discrimination since last week, with protesters torching a market, a jail and government offices in Papua.

EPA

The demonstrations were triggered by a racist slur against Papuan students, who were hit by tear gas in their dormitory and detained in the city of Surabaya on Indonesia's main island of Java on 17 August, but some protest rallies grew into a broader demand for an independence vote.

About 1,200 police officers have flown to the region which has a heavy military presence due to decades of separatist conflicts.

Jakarta has cut internet access in the region in the past week, to stop people sharing "provocative" messages that could trigger more violence, a step criticised by rights group and journalists, who said it had made reporting difficult.