The New Zealand based Indonesia Human Rights Committee says it is appalled at Australian Government statements that support for independence movements in Papua risks destabilizing the region.
Australian Foreign Minister Alexander Downer issued the warning during the inaugural Southwest Pacific Dialogue in Indonesia at the weekend.
He also said that the break up of Indonesia would be catastrophic for the region.
Maire Leadbetter of the Indonesia Human Rights Committee says the comments are very shocking and worrying, particularly when the Indonesian security forces have embarked on a new crackdown against the Papuan independence movement.
"Every time that someone likes Alexander Downer makes a comment like that about territorial integrity, it emboldens the Indonesian military in West Papua to feel that they can just carry on with impunity. So I'm really very shocked and disturbed by that attitude"
She says she welcomes the offer by New Zealand's Phil Goff to mediate between Jakarta and the Papuans.
Mr Goff says Indonesia is unlikely to take it up in the short term, but Ms Leadbetter says things take a while to come about and the New Zealand Foreign Minister should persist with the offer.