Ships and other vessels in Cuban territorial waters have been asked to withdraw, he said, as officials step up efforts to mitigate the epidemic.
Cubans have been told that face masks are mandatory on all public transportation nationwide.
In March, the island's government halted tourism, allowing in only Cuban nationals and resident foreigners.
Francisco Duran, director of epidemiology at the Ministry of Public Health, said the last commercial flight to Cuba on Wednesday came from the United States carrying 74 passengers, 73 of them Cuban nationals.
Currently, there are 12,370 foreign visitors quarantined at hotels and homestays in Cuba, according to the government.
On Thursday, Cuba reported 21 new cases of COVID-19, bringing the total to 233.