The Nuku'alofa Tourism Office said the order to refuse entry came from acting director of health, Reynald 'Ofanoa.
Three ships were to arrive in Nuku'alofa today - the Astor, Columbus, and Crystal Serenity.
A fourth vessel, a super-yacht Windstirid, was to call into Vava'u having sailed from Rarotonga.
The Astor is a German-registered vessel with 600 passengers; Columbus carries 1500 passengers and sailed from London while the Crystal Serenity is carrying 1000 passengers.
The cruise ships are reported to be heading for Suva and New Zealand waters.