The Melanesian Spearhead Group appears to have rejected the application for membership by the West Papua National Coalition for Liberation.
The coalition lodged its application over a year ago, and submitted documents of support from over seventy representative groups in Indonesia's Papua region.
However MSG leaders meeting in Papua New Guinea implied that West Papuans would need to re-apply for membership as an "inclusive and united" group.
PNG's prime minister Peter O'Neill says the group would also have to consult with Jakarta.
"We feel that it must be representative of all Melanesians that are living in Indonesia, and that the application be made in consultation with the Indonesian government just as we have done with FLNKS membership in the MSG."
A spokesman for the coalition, Andy Ayamiseba, has questioned the merits of consulting with Jakarta when he says it had attempted to sabotage their bid all along.
He also points out that the FLNKS didn't have to ask permission of France when it became a member of the MSG.