Around 500 people were expected to disembark on Wednesday, a health ministry official said, with the entire process completed by Friday.
"Day:15: Everyone here, thanks for your support over the last two weeks," tweeted one departing passenger from Hong Kong with the handle #quarantinedondiamondprincess. "If you ever find yourself quarantined in a windowless room but with access to WIFI, note you can count on people around the world to help."
NHK said that those who had roomed 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, Chief Cabinet Secretary Yoshihide Suga told a news conference.
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 on Wednesday morning on a chartered flight.
Asked why the Americans faced an additional two-week quarantine after returning home but Japanese leaving the ship did not, Suga said it was based on the advice of Japan's National Institute of Infectious Diseases (NIID).
The NIID said that based on the experience of those who returned from Wuhan, the epicentre of the epidemic, on charter flights earlier this month, there should be no obstacle to using public transport and the like if people had shown no symptoms such as fever for 14 days and had tested negative for the virus during the period their health was under surveillance.
Australian Prime Minister Scott Morrison said on Tuesday there were 220 Australians on board and that a total of 169 would be evacuated. Those evacuated will be flown to Darwin, where they will be quarantined for 14 days.
An Australian passenger said Australians had been told they would be pre-screened starting on Wednesday morning and taken to Tokyo's Haneda airport in the evening for an expected departure early Thursday.
"They told us to pack warm weather clothes for the two weeks in Darwin but who will have that after a cruise in the Japanese winter," passenger Vicki Presland told Reuters.
A captain's announcement on the liner said that Hong Kong passengers would also be evacuated over the next 24 hours and that according to information received, a Canadian charter flight would arrive on Friday morning.