The commander of the West Papua Liberation Army remains at large in the mountains of Puncak Jaya and is reportedly being pursued by Indonesia's military.
Human rights advocates in Papua province said seven people were killed last week by Indonesian security forces hunting down the commander, Goliat Tabuni, and his men.
Such operations have intensified this year after the Liberation Army declared war on the Indonesian state in January.
An Australia-based spokesman for the Liberation Army-associated Free West Papua Movement, Akouboo Amatus Douw, said after last week's surprise attack at Tabuni's stronghold in Tingginambut, Commander Tabuni fled into the bush.
"At the moment he is still in the bush, and also about thousands civilians also fled to the bush. So we don't know how many people been killed by Indonesian military forces, because it's very far and very remote area," he said.
The latest reports indicated that Indonesian forces were still in the Tinginambut area, attacking suspected Liberation Army members, which Mr Douw said was causing more displacement of villagers not linked to the conflict.
"We believe that because of the civilians, with mum and babies and kids also together with the group, it means it's a real emergency situation in terms of how they can get food or water."