The group, Human Rights Watch, says Indonesian security forces are still killing, torturing and raping civilians in their efforts to curb separatism in Papua.
In a report, the group says many serious rights violations occurred during police raids on communities believed to be harbouring separatist leaders or when security used force to break up gatherings.
The report alleges that in 2005 many civilians were missing or dead and tens of thousands were displaced from their homes after paramilitary forces burnt down houses in at least 13 villages in their search for separatists.
It says a culture of impunity is part of the problem in Papua where it says in the 14 incidents it documented, only one member of the security forces had faced prosecution.
A spokesman for Indonesia's national police, Sisno Adiwinoto, has denied any rights violations by police in Papua.
Jakarta places restrictions on access to Papua for journalists, diplomats and human rights organisations.