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.
Tonga has tightened cautionary measures concerning the coronavirus with health checks at the airport for incoming flights.
Extra caution has been exercised around cruise ships since the Diamond Princess was quarantined in Japan, when 135 passengers fell ill with the virus.
Meanwhile, the Northern Marianas has sent a sample from a patient suspected of having the coronavirus to the United States for testing.
However, the Commonwealth Health Care Corporation said the patient did not meet the full coronavirus case definition and the test was a precaution.
The corporation said CNMI had not had a confirmed case and its islands remained coronavirus-free.
It has also refuted a social media post alleging a man with the virus had arrived in the CNMI after escaping from a quarantine area in China.