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.