Kwalik's apparent death, yet to be confirmed by DNA testing, prompted protests across the town of Timika yesterday, with hundreds pouring on to the streets.

What led to Kwalik's death is unclear, not least because he held a meeting with the Papuan police chief, Bagus Ekodanto, only months earlier to discuss Mr Grant's death and the Freeport mine shootings.

He denied any role in the attacks, an assurance that Inspector General Ekodanto told The Age he believed.

But, according to national police spokesman Nanan Soekarna, police had recently received information from a man named as Simon Benai that Kwalik orchestrated a spate of sniper attacks near Freeport between July and November.

At least three died and more than a dozen were injured in the attacks, which shut down the mine, one of the world's most profitable.

Mr Benai's information also led them to a house in Timika early yesterday morning.

When the police arrived at 3am, they found Kwalik in a room in the back of the house, said Papuan police spokesman Lieutenant Colonel Agus Rianto.

''He held a revolver and he was pointing it at police,'' he said. ''We shot him in the thigh. He died at the hospital.''

Police said they believed the dead man was Kwalik, based on the testimony of five others in the house. DNA test results are expected shortly. But Kwalik is known to send others to meetings purporting to be him.

He was a legendary regional commander of the Organisasi Papua Merdeka (OPM) - Free Papua Movement - who controlled operations in the most volatile part of the province, the area centred on Timika that includes the highly controversial Freeport mine.

He was responsible for a series of militia actions against Indonesian security forces in West Papua and around the Freeport mine dating back to the 1970s. They included a raid that seized a group of western hostages in the mid-1990s and a spate of shootings and explosions around Freeport last year.

Police yesterday also alleged Kwalik was behind the 2002 murder of two US teachers near Freeport.

Paula Makabory, a West Papuan separatist exiled in Melbourne, described Kwalik as the ''true leader of the OPM'', who had recently embraced dialogue as the best path for indigenous West Papuans to achieve greater autonomy.

''He was part of the National Coalition for Liberation and he has supported peaceful dialogue with the Indonesian Government,'' she said yesterday.

''Whatever happened there, it's likely this incident will escalate … I suspect this is a deliberate attempt by security forces to escalate tensions.''

As news of Kwalik's death spread, hundreds of people took to the streets of Timika, protesting outside its small parliament and trying to blockade the airport, where Kwalik's body was taken in a closed casket to be flown to Jayapura and, possibly, Jakarta. Police blocked those trying to get to the airport.

''The situation is very tense,'' said Markus Makur, a journalist based in Timika.

According to Tom Beanal, an elder from the Amungme people of the area, the locals will be ''very angry'' if Kwalik's remains are taken from his home town.

Andreas Harsono, a researcher with Human Rights Watch, said Kwalik was the most charismatic of the OPM's leaders but he would soon be replaced.

Many indigenous West Papuans want independence from Jakarta, which seized the area following a disputed ''Act of Free Choice'' in 1969.