It comes amidst tensions in the region, and ahead of a state visit next month to Papua New Guinea by Indonesian President Joko Widodo.
Indonesia's state-owned news agency Antara reports Vice President Ma'ruf Amin met with Vanuatu's Deputy Prime Minister Jotham Napat in Jakarta on Monday.
Vanuatu has strongly supported the separatist push in West Papua for many years and Antara reports the issue of conflict in the province was discussed.
Amin announced a Papua Special Autonomy Development Acceleration Steering Committee had been formed to evaluate development in the Papua region.
"The granting of this special autonomy has been planned for the long term up to 2042," he said.
Amin said Indonesia respects the diversity in West Papua.
"I want to emphasise that the welfare approach will continue to become the main priority by respecting diversity and based on the principles of fairness, equity, and sustainability. The settlement of security issues is also done through a comprehensive approach," he said.
The Vice President said Indonesia is also ready to serve as a gateway for Vanuatu to enter the ASEAN market.
Vanuatu is hoping to forge a technical cooperation agreement as well as establish sister city and provincial partnerships.
At Monday's meeting, Napat stated that his visit to Indonesia is a fundamental step to recover trust and to express eagerness to build sound cooperation between Vanuatu and Indonesia.
Napat also echoed his country's keenness to forge a technical cooperation agreement between both nations as well as to establish sister city and sister province partnership that he said can be started with Papua Province.