Tom Allard – Indonesia's human rights commission has urged Jakarta to address grievances of indigenous West Papuans as it announced an extensive investigation into a crackdown by security forces that caused at least six deaths, following a protest rally.

The Indonesian government and security forces continue to defend their actions against what they described as a "coup d'etat".

Police and soldiers dispersed a rally of several thousand West Papuans on Wednesday, firing weapons and detaining and beating participants after a declaration of independence by the Third Papuan People's Congress.

"We deeply regret the violence and killing on Papuans done by TNI [Indonesian military] and police apparatus," said Ridha Saleh, deputy commissioner at the independent human rights body.

"We regret the application of security approach against congress participants because it is this security approach that has disturbed all attempts to bring peace to Papua and attempts to establish a dialogue long sought by both Papuans and the government."

At least two of the bodies of the dead were found dumped behind a military post and at least three of the scores injured suffered gunshot wounds.

Andreas Harsono from Human Rights Watch said autopsies had revealed three of the dead had also been shot, contradicting assurances by police and military that they only fired warning shots.

Co-ordinating Minister for Security Djoko Suyanto justified the tough action, saying, "The police raided the rally because it was already considered a coup d'etat. They declared a state within a state and did not recognise the President of Indonesia."

Most of those arrested have been released, but the senior figures involved in the congress remain in detention. They include Forkorus Yaboisembut, head of the Papuan Customary Council.

Foreign journalists cannot travel to the region without special permission and were banned from covering the congress.