Indonesia's security forces have been intensifying a military crackdown in the Papua highlands following the killing of the province's intelligence chief by rebel groups in late April.

His death angered Jakarta who moved to officially designate Papuan separatists "terrorists".

Chief security Minister Mahfud MD said rebel groups killed two patrolling soldiers in Dekai district in Yahukimo regency on Tuesday.

"The attack shows that the terrorist groups continue to commit violence in Papua," he told a Jakarta press conference on Wednesday.

Four other security forces were wounded in a separate attack on the same day in Serambakon district in Bintang mountains regency, he added.

"The government is committed to completely quell the groups in Papua," he said.

Rebel group spokesman Sebby Sambom said Wednesday the separatist movement was responsible for the killing of the two soldiers.

At least three soldiers and nine rebels have died in military and police attacks after the death of Papua's intelligence agency chief on April 25, according to Indonesian officials.

Papuan separatists have claimed responsibility for his killing, with President Joko Widodo last month ordering security forces to crack down on the rebels.

Indonesian security forces have been dogged for years by allegations of widespread rights abuses against Papua's ethnic Melanesian population, including extrajudicial killings of activists and peaceful protesters.

A former Dutch colony, Papua declared itself independent in 1961, but neighbouring Jakarta took control two years later promising an independence referendum.

The subsequent vote in favour of staying part of Indonesia was widely considered a sham.