Japan's health ministry said it had discovered 79 additional cases of the flu-like disease that originated in Wuhan, China. Of the new cases, 68 showed no symptoms, it said.
About 500 people were expected to disembark the Diamond Princess on Wednesday, a ministry official said earlier, with the process completed by Friday.
The ship, operated by Carnival Corp, was quarantined after arriving in the port of Yokohama on Feb. 3, after a man who disembarked in Hong Kong before it travelled to Japan was diagnosed with the virus.
It originally carried some 3,700 passengers and crew. Many of the infected people have been taken to hospital. About half the passengers are Japanese.
"Day:15: Everyone here, thanks for your support over the last two weeks," a departing passenger from Hong Kong said on Twitter, using the tag #quarantinedondiamondprincess.
Japan ranks second in the world after China for the number of confirmed virus cases because of the outbreak on the ship, which is the biggest cluster of infections outside China.
Japan has come under fire for its handling of the ship's quarantine, although top government officials have defended it.
"Unfortunately, cases of infection have emerged, but we have to the extent possible taken appropriate steps to prevent serious cases, including sending infected people to hospital," NHK quoted Health Minister Katsunobu Kato as telling a parliamentary panel.
The United States evacuated more than 300 nationals on Monday on two chartered flights and six South Koreans and one Japanese spouse flew to South Korea early on Wednesday on a chartered flight.
The Americans flown home will have to complete another 14 days of quarantine.
Australian Prime Minister Scott Morrison said there were 220 Australians on board and a total of 169 would be evacuated. They will be flown to Darwin, where they will be quarantined for 14 days.
Hong Kong has also said its residents coming home will have to spend 14 days in quarantine.
Japanese people getting off the ship can go directly home.
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The U.S. Centers for Disease Control and Prevention (CDC) said the quarantine "may not have been sufficient to prevent transmission among individuals on the ship".
The rate of new infections on board, especially among those without symptoms, was a risk, it said.
More than 100 Americans remain on the ship or in hospital in Japan, the CDC said.
The CDC said anyone getting off the ship and hoping to travel to the United States would have to wait 14 days without symptoms or a positive coronavirus test.
Japan's chief cabinet secretary, Yoshihide Suga, asked at a news conference why Japanese leaving the ship did not have to spend another two weeks in quarantine, referred to the advice of Japan's National Institute of Infectious Diseases (NIID).
The NIID said there should be no problem if people had shown no symptoms for 14 days and had tested negative for the virus during the period their health was under surveillance.
NHK said that those who had shared rooms with passengers who tested positive would have to stay on the ship another 14 days from the time the infected roommate left.
Crew members, who have been sharing rooms, would move to separate rooms and undergo health checks, it said.
An Australian passenger said Australians had been told they would be pre-screened from Wednesday and taken to Tokyo's Haneda airport for an expected departure early on Thursday.
A captain's announcement on the liner said that Hong Kong passengers would also be evacuated over the next 24 hours and a Canadian charter flight was expected on Friday.
Italy, Israel, Britain and Taiwan were also preparing to evacuate their nationals, Suga said.Besides those on the cruise liner and returnees brought home from Wuhan city, about 60 cases of domestic infections have been confirmed in Japan, including 22 in Tokyo, NHK said.