The Indonesian President Susilo Bambang Yudhoyono has defended the actions of the country's military in Papua province.
Three people were killed in October as police and military tried to disperse a political meeting in Abepura.
The government's national human rights commission found strong evidence of excessive acts that led to rights violations.
Human Rights Watch and other rights groups have called on U.S. President Barack Obama to address the issue when he met Indonesian President Susilo Bambang Yudhoyono in Bali during an East Asia Summit.
But Mr Yudhoyono says there is accountability and military personnel who commit crimes will be investigated.
He says the world must know that there are armed cells in Papua, and if soldiers are doing self-defense then it can't be categorised as violating human rights.