The separatist group, the West Papua National Coalition for Liberation, has called on Vanuatu to reconsider its foreign policy in regard to Indonesia.
The Coalition's John Ondawame made the call after an Indonesian military aircraft arrived with equipment for next month's Port Vila summit of the European Union with its development partners in the African Caribbean and Pacific region.
Indonesia has become an observer of the Melanesian Spearhead Group, which includes Vanuatu that had been the only country to support the Papuans' quest for self-determination.
In view of the Papuans' plight over the years, Mr Ondawame says Vanuatu should revisit its dealings with Jakarta.
"We firmly believe that the Vanuatu government signed a co-operation agreement with a very brutal regime in the Asia Pacific region that killed thousands of my people in West Papua."