Documents leaked from the Indonesian Army's Special Forces unit, Kopassus, have revealed that the group targets churches in Papua and defines civilian dissidents as the enemy.
The documents describe a covert network of surveillance, infiltration and disruption of Papuan institutions.
Among the leaked information is a list of Kopassus enemies, headed by Papua's top Baptist minister, Socrates Sofyan Yoman.
Also included are activists, traditional leaders, legislators, students and intellectuals.
Damien Kingsbury of Deakin University says Kopassus is at the forefront of the secuirity forces' ill-treatment of Papuans.
"If they raise concerns, quite legitimate concerns, about the way their homeland is being exploited and ravaged by external interests and often illegally, I might add, and often illegally by the armed forces itself, if they raise these concerns, they are then subject to very considerable pressure, often intimidation or violence."