The killings were a marked escalation from decades of mostly sporadic skirmishes between poorly armed and disorganised guerrillas and a powerful Indonesian military accused of human rights abuses against civilians.

Governor Lukas Enembe said the presence of Indonesian security forces in the predominately Christian area was preventing residents from celebrating Christmas.

"I, as the governor of Papua, am asking President Jokowi to withdraw all the troops in Nduga," he told reporters late Thursday, using President Joko Widodo's nickname.

Local media reported Yunus Wonda, chairman of the Papuan parliament, saying some residents of Nduga had fled into the forest following army operations in the area.

The military said it would not be withdrawing troops and dismissed claims villagers had fled in fear.

"We're there to protect them," Papua military spokesman Muhammad Aidi told AFP.

Victims of the massacre -- employees of a state-owned contractor -- were building bridges and roads in a major infrastructure push for Indonesia's most impoverished region.

The rebels claimed the project was military controlled and the workers were legitimate targets.

At least four more workers remain missing, while a soldier was also killed by rebels, according to authorities.

Enembe said an independent task force would be formed to investigate the killings.

The former Dutch colony declared itself independent in 1961, but neighbouring Indonesia took control Papua two years later on the condition it hold an independence referendum.

Jakarta annexed the mineral-rich region in 1969 with a UN-backed vote that was widely seen as a sham.

The rebels have vowed to continue their insurgency and to fight for an independent Papua, which shares a border with the island nation Papua New Guinea, just north of Australia.