The West Papua National Coalition for Liberation says the Indonesia visit by the foreign ministers from the Melanesian Spearhead Group has defeated the mandate given at the last MSG summit.
The ministers were tasked to visit Papua to vet a formal application by the Coalition to become an MSG member.
The visit to Papua's capital only lasted a few hours and was marred by dozens of arrests.
The Coalition's vice-chairman, Otto Ondawame, says the purpose of the visit was defeated.
"Without meeting affected people, particularly the resistance movement, tribal council, women's organisations -civil society at large. This shows clearly to the world that Indonesia is not serious with the request by the MSG leaders during the summit in Noumea of June 2013."
Otto Ondawame says Indonesia shifted the visit to one about economic co-operation.
Vanuatu pulled out of the visit, just days before it was to go ahead.