Violence has flared in the capital of Indonesia's troubled province of West Papua as security forces moved to break up a flag-raising ceremony by independence supporters, a Sydney-based human rights monitor said today.

Five people were shot and wounded and at least 18 people arrested as 100 police dispersed the gathering at Trikora soccer field in Adepura, a suburb of Jayapura, just before 4.00pm (AEST) today, John Rumbiak, international spokesman for the Papuan human rights group Elsham, said.

Mr Rumbiak, who is now based in Sydney, said an Elsham human rights worker who witnessed the demonstration had been beaten as he tried to photograph the clash.

Two of the event organisers had also been beaten by police as they were taken away on a police truck for interrogation in the city centre, Mr Rumbiak said, quoting a report by phone from his colleagues in Jayapura. Another 16 people were being questioned at the local Adepura police station.

Among the five people wounded were 20-year-old Marselina Gobay, who was shot in the leg, and 24-year-old Yermia Kayame, shot in the head. The five people suffering gunshot wounds were being treated at a local hospital, Mr Rumbiak said.

December 1 commemorates the first West Papuan national congress in 1961, organised by the then ruling Dutch as a preparation for independence. Last week, Indonesian authorities had warned activists not to raise their distinctive blue, white and red Morning Star flag today.

"The concern is that this is a peaceful demonstration and from a human rights perspective it has to be allowed to take place," Mr Rumbiak said. "It is freedom of expression."

Mr Rumbiak said the demonstration had been calling on newly-elected Indonesian president Susilo Bambang Yudhoyono to initiate a peaceful dialogue between the government and independence supporters.

Last month human rights advocates in Australia and Indonesia said a fresh military crackdown in the heavily-forested highlands district of Puncak Jaya had left eight people dead and forced thousands of locals tribespeople to flee their villages.

Indonesia's resource-rich easternmost province, formerly known as Irian Jaya, has been the site of sporadic violence since the early 1960s when Indonesia assumed control from the Dutch.

There were now more than 25,000 troops based in the province after a build-up over the last two years, Mr Rumbiak said. Journalists are banned from entering the province.