An Australia-based academic has called for the role of Indonesia's security forces in Papua to be clarified.
The Age newspaper reports Victoria University researcher Richard Chauvel as saying the Indonesian army, or TNI, is exploiting prejudices against indigenous Papuans so it can remain in the impoverished region.
Mr Chauvel told this week's Australia Indonesia Governance Research Partnership forum in Jakarta that the TNI retains a stronger presence in Papua's troubled Central Highlands than the local government does.
Troop numbers in Papua have increased in recent years, with the International Crisis Group estimating there are 12,000 Indonesian troops in Papua, and 2,000 to 2,500 paramilitary police.
The Free Papua Movement has been fighting for an independent Papua since the 1960s.
In July, Human Rights Watch said that the security forces still killed, tortured and raped civilians to curb separatism.
Richard Chauvel said the military is determined to keep the region closed to outsiders, keeping Central Highlands as their stronghold.
A Papuan government source says the military in Papua receive direct orders from Jakarta, but its activities often clash with central government policies.