Gunfire exchanges between Indonesian military forces and West Papuan guerillas in Mimika regency have left three people dead since Sunday.
The death of a soldier with the Indonesian army, or TNI, prompted renewed fighting in the mountainous area around the Freeport mine in Papua province.
TNI and police forces had gone into a remote part of the area to reclaim villages controlled by the West Papua Liberation Army, or TPN.
TPN guerilla forces have declared war on the Indonesian state and the operations of the Freeport mine.
An NGO worker in Mimika's capital Timika, Demi Picoalu, said the TNI killed two Papuans in an intense sweep operation sparked by the killing of one of their troops on Sunday.
"After that, massive sweeping operation in (local) villages, and they (joint TNI and police troops) shoot everyone, because the TPN is hiding in the community village, so TNI used rockets."
Earier, according to the Jakarta Post, the TPN said that over 1,000 civilian lives were at risk due to the TNI's operation.
TPN spokesperson Hendrik Wanmang said they had gathered civilians in Kampung Opitawak and TPN fighters had retreated and left the kampung to avoid civilians being mistaken for armed fighters.
However, Demi Picoalu said that according to reports he had received from Banti village, the TNI's sweep operation had stopped.
Local villagers had been evacuated to the relative calm of a village named Banti 2 where they were considered safe lest fighting break out again.