Kwalik's body was to be put on display for mourners to see but it was not immediately clear when the funeral would take place.

Police shot Kwalik dead Wednesday amid suggestions he was the leader of the Free Papua Movement (OPM), a shadowy militia that has been fighting for independence from Indonesia for decades.

"Though Kelly Kwalik has died, his vision will be alive forever for Papuan people," read one banner as they shouted angrily for independence.

"We have lost our respected leader that had sacrificed his life for our independence," protester Thomas Wamang told AFP.

"But there are still many from Papuan's young generation that will continue our struggle for independence."

Police said Kwalik had been hunted after unidentified gunmen launched a string of ambushes near Timika over the past six months targeting the operations of US miner Freeport McMoRan.

Freeport's giant Grasberg mine, which sits on one of the world's biggest gold and copper reserves, has long been linked to human rights abuses involving Indonesian troops who secure the facility.

Australian mine technician Drew Grant was killed in one of the attacks in July.

Kwalik, 60, reportedly claimed responsibility for the shootings but his associates have denied this. Others have speculated that the ambushes are the work of rogue Indonesian police or soldiers seeking more money from Freeport.

Kwalik stood accused of multiple killings and kidnappings dating back to the mid-1980s.

The poorly armed OPM has waged a low-level insurgency -- often using bows and arrows rather than guns -- against Indonesian rule of the resource-rich, ethnically Melanesian region since 1964.

A political analyst from the Indonesian Institute of Sciences, Muridan Widjojo, called on the Indonesian government to open dialogue with Papuan people to prevent any backlash.

"Kwalik's death will intensify the Papuan people's struggle for independence," the analyst said.

"There will be a growing distrust among Papuans towards the central government. This is a strong reason why a peaceful dialogue becomes an urgent need."