Indonesia's human rights watchdog may launch an investigation in Papua following fighting which has left eight people dead and forced thousands to flee gunmen said to be covert members of the notorious Kopassus commando unit.

A coalition of activists, churches and student organisations last week urged Indonesia's National Commission on Human Rights, known as Komnas HAM, to set up a fact-finding team to investigate a series of shootings in the separatist province.

Eight people, including a church minister and a police officer, were killed in a series of attacks by unidentified gunmen between August 17 and November 12 this year in Puncak Jaya regency. Another 15, mostly children, died when more than 5,000 residents from 27 villages fled into the forests fearing further attacks by the gunmen, the coalition said.

Aloysious Renuaren, from the Jayapura-based rights group Elsham, said local people believed the gunmen were members of Kopassus. The feared 5,000 strong unit has a notorious rights record, which includes training the militia forces behind the 1999 East Timor post-independence vote bloodbath.

"We believe that Kopassus is involved," Renuaren told AAP. "Kopassus is here, but they came in to do military intelligence operations, so we don't know how many there are. Most of them are not wearing uniform so people cannot recognise them, but because of their military operations in Puncak Jaya around 5,000 local people cannot eat and are now surviving on grass in the jungle."

The police and military are blaming separatist rebels belonging to the Free Papua Movement for the shootings. But rights activists, tribal and religious leaders blame the military.

Kopassus troops were recently redeployed to the province to quell an increase in separatist activities after earlier being withdrawn following revelations Kopassus personnel were involved in the 2002 killing of independence leader Theys Hiyo Eluay. An Elsham spokesman in Australia recently accused the military of trying to "East Timorise" the province of Papua by stirring unrest.

Komnas HAM member Lies Sugondo said the watchdog had been looking closely at Papua and had already investigated earlier military and police abuses there. "We have to review it," he told Kompas newspaper. "But it will need money to investigate and we have to look first at whether it is available." Puncak Jaya regent Eliezer Renmaur said he would support an investigation.

Human rights groups have asked Indonesia's new President Susilo Bambang Yudhoyono to pull troops out of Puncak Jaya as the first step to a peaceful solution for the province.

Separatists have waged a low-level struggle against Jakarta since Indonesia took over Papua from Dutch colonial rule in 1963 following a referendum widely seen as rigged.