The Papua Presidium Council is appealing to Free Papua or OPM rebels to refrain from attacking the Indonesian military so it can continue efforts to establish dialogue with Jakarta.
Council member, Franz Albert Joku, says there are government members who are willing to discuss Papua's political status but attacks by OPM rebels could jeopardise that.
Earlier, reports from Jakarta say 15 suspected OPM rebels broke into a army arsenal at Wamena, sparking a gunfight in which three people, including two soldiers, were killed.
In response to the raid, the Indonesian Army's Chief of Staff has ordered the military to quell the OPM.
Mr Joku says while it is not clear whether OPM rebels were involved, he is calling on them not to jeopardise the small support Papuans have within government.
"We would appeal to the OPM fighters to give the council a chance to see what we can do in terms of pushing ahead with peaceful dialogue. It is getting some support in some quarters within the Indonesian government to sort out the Papuan political dispute."
Franz Albert Joku from the Papua Presidium Council