The OPM Free Papua Movement says 14 of its members died when Indonesian police raided one of its bases in Paniai regency this week.
The Jakarta Globe reports OPM Paniai spokesman, Leo Yeimo, as saying that the group has evacuated its former base in Eduda.
The site has since become a police base.
There's been an increased presence of security forces over recent weeks in Paniai for a campaign to hunt Papuan separatists.
Hundreds of Brimob paramilitary police have joined four full battalions of Indonesian troops deployed in an offensive to surround the OPM stronghold.
Mr Yeimo says villagers are being constantly attacked by security forces on land as well as from helicopters.
Radio New Zealand International has received reports of forcible evacuations and the displacement of thousands of people.
A police spokesman Commander Wachyono says he could not confirm the OPM claims of casualties, and that the OPM instigated the attack.