Eight people on the vessel, which arrived at Yokohama Bay on Monday, have symptoms such as fever, top government spokesman Yoshihide Suga said.
Television footage showed several quarantine officers boarding the Diamond Princess cruise ship at the port of Yokohama on Monday evening to check all 2,666 passengers and 1,045 crew.
The move comes after an 80-year-old passenger who disembarked on January 25 in Hong Kong tested positive for the virus, which has killed 425 people in China.
The man "did not visit a medical centre inside the ship while he was sailing with us," cruise operator Carnival Japan said in a statement.
"According to the hospital where he is staying, his condition is stable and infection was not found among his family members who sailed with him," the statement said.
A woman in her twenties who was sailing with her mother on the ship told private broadcaster TBS on Tuesday that all passengers "were asked to stay in their rooms to wait for virus tests".
She said they had been waiting since Monday and had no word of when they would be tested as of early Tuesday.
The vessel's departure from Yokohama would be delayed by at least 24 hours to Wednesday or later, Carnival Japan said.
The cruise ship had already been through a quarantine procedure on Saturday at a port in Naha in Japan's southernmost prefecture of Okinawa, and quarantine officials had issued certificates allowing passengers and crew to land, Suga said.
A health ministry official said no one on board at that time showed any symptoms and the case of the man who disembarked in Hong Kong was not known at that time.
But after his case emerged, a second quarantine was organised.
"Quarantine officials at Naha told us to cancel the (certificate for landing) and carry out a second quarantine as we can't rule out the possibility of infection" after the passenger who got off in Hong Kong tested positive, he said.
Quarantine officials are now checking the condition of everyone on board and testing those with symptoms of illness for the new coronavirus, as well as other infectious diseases, including malaria and Dengue fever, a second health ministry official told AFP.
The decision on whether to allow the vessel to dock at Yokohama port and let passengers land on Japanese soil "will be made at the quarantine station", taking into consideration the WHO's estimate of a 10-day incubation period, Suga said.
Since Saturday, Japan has been barring foreign nationals who have been to Hubei in recent weeks, as well as holders of passports issued in Hubei -- the Chinese province at the epicentre of the crisis.
Arrivals displaying symptoms of the new virus can also be denied entry.
A total of eight foreigners have been barred from entering so far, Suga said on Monday.
The health ministry said as of Monday that 20 people in Japan have tested positive for the new virus, of whom four showed no symptoms.
Japan has flown more than 500 citizens out of Wuhan, where the coronavirus originated.
(Only the headline and picture of this report may have been reworked by the Business Standard staff; the rest of the content is auto-generated from a syndicated feed.)