Reports from Indonesia's Papua region say more than 40 West Papuans were arrested during the visit by the Melanesian Spearhead Group in Jayapura.
The MSG Foreign Ministers made a fleeting visit to the Papua provincial capital and has brief meetings with the Governor and the Papua regional legislature.
However, Tabloid Jubi reports that dozens of activists were arrested by Indonesian police outside the legislature for demonstrating against the lack of access that the West Papuans have been granted to the MSG.
This comes after Vanuatu's government withdrew from the mission, saying it felt Indonesia was not allowing the foreign ministers access to the people who the MSG sought to meet.
The visit is part of an effort to vet a formal bid for MSG membership by the West Papua National Coalition for Liberation.
The head of the MSG delegation, Fiji's foreign minister Ratu Inoke Kubuabola, has rebuffed the separatists' aspirations, saying the ministers fully respect Indonesia's sovereignty and territorial integrity and further recognise that West Papua is an integral part of Indonesia.