An Indonesian government spokesperson says police and military officers didn't abuse power or mismanage security around last week's third Papuan People's Congress in Jayapura.
The congress ended in chaos when it was broken up by soldiers and police after the delegates announced the establishment of the independent state of West Papua.
There are unconfirmed reports that at least seven people died.
The Jakarta Post reports Julian Aldrin Pasha saying the security forces completed their duties as required by their mandate.
He told the paper that initially the government had no problem with the plan for the congress.
But he says when it turned into a forum that didn't recognise the government and the Republic of Indonesia, something had to be done.
The spokesperson says any attempt to secede from the country is against the law.
The government has denied that its security forces were involved in the killings.
But Julian Aldrin Pasha is promising an internal investigation if any security personnel are shown to have violated their code of conduct.