The West Papua National Liberation Army, or TPN, has told villagers in Mimika regency their conflict is not with them but with Indonesian security forces.
Police blamed the TPN, which it refers to as a criminal group, for shootings near Tembagapura and the Freeport mine since August.
One policeman was killed and several injured.
A tense standoff has developed, with police and military accusing the TPN of holding 1300 people hostage.
The TPN, which recently declared war on the Indonesian state, denies this.
A spokesman for the Justice and Peace Secretariat in Mimika's capital Timika, Saul Paulo Wanimbo, said the TPN had relayed a message to local villagers.
"TPN say to people, we have no problem with you, we always have problem with military and police. If we went to war, we went to war against police and military only. They say that to the peple in Tembagapura area."
Mr Wanimbo said Timika was generally peaceful, but that Indonesian security forces have been busy flying personnel into the area.
"They always send military amd police every night by plane from Java, Sulawesi or Maluku to here, to Timika. Every night we hear the plane sounds arrive and go from Timika."
He said there were also many Indonesian intelligence officers in Timika and in the area around the Freeport mine.
Freeport has temporarily shut the main supply route to its Papua mine amid the escalating tensions.
Indonesian officials on Saturday said about 200 police and military personnel had been deployed in preparation to secure the area by force, if necessary.