The last batch of Japanese passengers to leave the ship will be quarantined for two weeks near Tokyo.
Some 100 passengers who were in close contact with infected people on board began disembarking from the coronavirus-stricken Diamond Princess cruise ship on Saturday, local media said.
They included the last batch of Japanese passengers to leave the ship while some foreign passengers were still waiting on board for chartered aircraft to be sent by their governments. Around 970 passengers disembarked earlier this week.
Television footage showed a driver in a white protective suit at the wheel of a bus with the curtains drawn so that passengers could not be identified.
They will be quarantined for two weeks near Tokyo, officials said.
With the disembarkation, a 14-day quarantine is expected to start for more than 1,000 crew still on board as many of them did not undergo quarantine because they were needed to keep the ship running.
They were preparing food and delivering meals to cabins, leading some critics to charge they were inadvertently spreading the virus throughout the ship, which has seen more than 600 cases of the potentially deadly COVID-19 disease.
Health minister Katsunobu Kato on Saturday defended Japan's on-board quarantine, saying there was no medical facility large enough to admit more than 3,000 people at once.
Meanwhile, Kato said Japan was considering using the anti-influenza medication Avigan to treat patients.
"We will check if various medicines, led by Avigan, can be effective," Kato told a TV programme, saying the government would push for their use if they are confirmed to be effective.
Outside the Diamond Princess, Japan has seen 105 cases of the new coronavirus.