Hundreds of supporters have rallied in the town every day since his death, calling for independence from Indonesia and briefly clashing with police outside a local parliament building where the coffin was on display.

The casket was draped in the outlawed "Morning Star" flag of Papuan independence, a daring show of defiance given that anyone waving the separatist standard faces up to life in prison under Indonesian law.

Dozens of heavily armed Indonesian police and troops were standing guard outside the building, where a brief riot broke out on Saturday as protesters pelted security forces with stones and warning shots were fired.

Timika's Catholic bishop, John Philip Saklil, called Kwalik a "great figure who fought for the best for the Papuan people", as he led the funeral mass in the parliament compound.

In an emotionally charged speech to about 600 people gathered outside parliament, Papuan rights defender and Kwalik's aunt Yosepha Alomang rejected suggestions Kwalik was a terrorist.

"Kelly Kwalik was a commander. He was not a terrorist, he was not a provocateur. He never committed violence," she said.

OPM fighters, sometimes using bows and arrows and World War II-era explosives, have waged a low-level insurgency against Indonesian rule of the resource-rich, ethnically Melanesian region since the 1960s.

Police have linked Kwalik to a string of ambushes near Timika over the past six months targeting the operations of US miner Freeport McMoRan, one of which killed an Australian mine technician.

Kwalik however denied any role in the attacks, which some analysts suspect were the work of rogue police or soldiers trying to extract protection money from Freeport.

Freeport's giant gold and copper mine has long been linked to human rights abuses involving Indonesian troops who secure the facility.

In 2002 two of Kwalik's men allegedly killed two US Freeport employees.

In 1986 his followers allegedly kidnapped and killed eight Javanese students. He was also accused of ordering the kidnapping of 12 scientists -- four Indonesians, four Britons, two Germans and two Dutch -- in 1996.

Two of the Indonesians were killed in a military rescue operation that freed the other hostages after three months.

In 2001 he is said to have ordered the kidnapping of two Belgian journalists who were released after two months.