The ship, Braveheart, carried a marine science team from New Zealand around the islands, over which Vanuatu and France are locked in a protracted dispute.
The uninhabited islands have been claimed by both countries for decades, after France annexed them for New Caledonia shortly before Vanuatu was granted independence.
The New Zealand team led by the Auckland War Memorial Museum had asked the government in New Caledonia if it could carry out research in the area, but not Vanuatu.