Reports from Indonesia say three members of the West Papua National Committee, or KNPB, have been charged with subversion.
This comes after the pro-independence organisation was forced from its secretariat in Timika last Thursday by dozens of police and soldiers.
Police had alleged they'd committed subversion or treason.
But the KNPB members have said they were holding a pray service.
CNN Indonesia reported that the KNPB secretariat remained under police control.
A lawyer for the KNPB said the Indonesian police acted illegally in storming the secretariat.