The KNPB said its headquarters in Jayapura and Asmat were shuttered by military and police in December.
On Thursday, committee members in the Southern city of Timika were forced out of their offices by at least 80 officers.
It will now be used as a joint military-police post.
Edo Dogopia, a member of the group based in Timika, said he's afraid other locations in Papua could be targeted as well.
"I am feeling worried because this is our place.
"We are indigenous people but they say you don't stay here, you go to your place. We will not go to anywhere because this is our place."
Mr Dogopia said around 30 KNPB members were camping on the road outside the Timika office and would not leave, despite the takeover.
"We are stay in front of our office but we have intimidation and Indonesian police come and angry to us, but we never come back from our commitment," he said.