Indonesia's military (TNI) has given an ultimatum to the West Papua Liberation Army to surrender.
The Liberation Army claimed responsibility for killing up to 31 Indonesians, mainly road construction workers, this month in the Highlands of Papua province.
TNI and police have retrieved 16 bodies from Nduga regency, having deployed a major joint operation there in response to the massacre.
A TNI spokesperson Mohammed Aidi said that the Liberation Army should immediately surrender or be finished.
Colonel Aidi has denied media reports that the military is using aerial bombing against Papuan communities in the Liberation Army's stronghold area.
He said at present the joint forces have captured and occupied Nduga's Yigi and Mbua districts, and that villagers who fled from fighting to the bush are starting to return.
The TNI's response to the massacre has reportedly caused four fatalities among civilians, according to local media.
However, Colonel Aidi said that given the area where casualties were reported, it was unlikely they were pure civilians but rather those linked to the perpetrators of the massacre.
Colonel Aidi disputed claims by a Liberation Army spokesman that the TNI has breached an agreed combat zone in this escalating conflict.
Referring to the Liberation Army as an armed criminal group, he said its style is guerilla fighting which knows no limits, accusing it of cowardice.
The TNI has also urged Papua's provincial and district governments to not be silent about the conflict.
Colonel Aidi said it was the duty of such office holders to honour their commitment to the Unitary State of the Republic of Indonesia based on Pancasila and the 1945 Constitution.