A US-based Papuan journalist and academic, Octo Mote, says the Indonesian Army's Special Forces unit, Kopassus, operates only under its own agenda in Papua.
His comment comes as reports of leaked Kopassus documents reveal that the group targets churches in Papua and defines civilian dissidents as the enemy.
The documents regard as enemies people such as church leaders, activists, traditional leaders, legislators, students and intellectuals.
They also describe a covert network of surveillance, infiltration and disruption of Papuan institutions.
Octo Mote says even a military commander in Papua cannot control Kopassus.
"Because they have a straight line to Jakarta and he [a military commander] doesn't have a highest link except through the command line which is weak in Indonesia because in the military in Indonesia, it's more based on personal and gang relations rather than structure."