Louise Williams – Thousands of protesting tribespeople in the remote Baliem Valley raised an independence flag early this morning, as pro-independence demonstrations in Irian Jaya widened despite a bloody police crackdown at a similar ceremony on the island of Biak yesterday.

Diplomatic and church sources confirmed that up to six people had died and as many as 140 were wounded when police opened fire with rubber bullets and live ammunition on the island of Biak yesterday, where hundreds of Irianese refused to take down an independence flag.

The armed forces commander, General Wiranto, warned the military would take "firm action", saying the hoisting of any flag, other than an Indonesian flag, was tantamount to "a revolt against the Government". "If there is an act of hoisting a different flag, it means they are trying to break up the nation. This means a betrayal of the nation. The Indonesian armed forces cannot tolerate this and will take firm action.

Shops and offices were closed and witnesses contacted by phone said troops patrolled the streets of Irian Jaya's main towns today after a series of pro-independence protests that began in the provincial capital of Jayapura last week. Church sources said they expected protests to continue and expressed fears of further violence.

The Indonesian Government is now facing major pro-independence protests in both East Timor and Irian Jaya, where indigenous people have long complained of second-class treatment by Jakarta's officials, human rights abuses by the Indonesian armed forces, and the domination of the local economy by Government-assisted transmigrants from other parts of the archipelago. Pro-independence groups have seized on the change of Government in Jakarta as an opportunity to express their grievances.

The armed forces today denied there had been any deaths in Biak yesterday but the regional military commander, Colonel Agus Edyono, conceded live ammunition had been used as well as rubber bullets. Church sources said between five and six people died and diplomatic sources said "at least one, and probably more" people had been killed when a crowd of some 700 refused to lower an independence flag flying over the Biak port. A mobile brigade was brought in to boost troop numbers on the remote island, which is surrounded by coral reefs and pristine turquoise waters.

Mr Paul Baut, of the Legal Aid Institute in Jayapura, said 141 people were injured, of whom three had been confirmed dead, and an overnight curfew was imposed.

Colonel Edyono said live rounds were fired into the air, but protesters were hit by ricocheting shots. "These people were not demanding reform, they wanted a separate state. We, and civic leaders, had pleaded with the group to take down the flag since last week, but they refused," he said. Hundreds of students were today holding a vigil at the Jayapura Hospital where a law student remained in a critical condition after being shot in the head during a protest last week.

In Canberra, the Australian Government urged Indonesian forces in Irian Jaya to show restraint, AAP reported. A spokesman for Foreign Minister Alexander Downer said Australia was obviously concerned by the reports. "The embassy in Jakarta is seeking clarification about what has happened," the spokesman said. "Naturally at this time we would urge restraint on all sides in this issue."