Young people on the island of Mare put up banners opposing ship visits, which prompted the island's contractor to cancel the stop-over as a precaution.
Mayor Pierre Ngaihoni said missing the ships' visits, from Australian company Carnival, would have an impact on stall holders.
Last month, New Caledonia's authorities banned access for ships with people onboard showing symptoms of the coronavirus.
A planned charter flight from China to Noumea last week was also cancelled, purportedly because of problems finalising documentation.