Two elderly passengers from the quarantined Diamond Princess ship had died of the disease, Japanese public broadcaster NHK reported. The passengers were a man and a woman in their 80s, NHK said, citing an unidentified government source.
In Japan, the government has come under intense criticism for its handling of an outbreak on a cruise ship carrying about 3,700 people, that was placed in quarantine off Yokohama on February 3.
A second group of about 600 Japanese and foreign passengers from the Diamond Princess was set to disembark on Thursday, after the first batch were released from quarantine a day earlier.
Hundreds of people who left the chip on Wednesday were placed in quarantine again in their home countries, with Australia and Hong Kong putting their returned citizens in supervised isolation for another two weeks.
Passengers arriving in Hong Kong were taken straight into quarantine at a new public housing estate. A contingent of Australian evacuees were placed in quarantine at an old mining camp outside Darwin in the country's far north.
Even as the first passengers disembarked on Wednesday, Japanese authorities announced 79 new cases had been discovered on board, bringing the total to at least 620, over half of the known infections outside mainland China.
From the start, experts raised questions about quarantine on the ship. Passengers were not confined to rooms until February 5. The day before, as passengers were being screened, ship events continued, including dances, quiz games and an exercise class.
The U.S. Centers for Disease Control and Prevention (CDC) said Japan's efforts "may not have been sufficient to prevent transmission among individuals on the ship."
Japanese Health Minister Katsunobu Kato defended Tokyo's efforts.
"Unfortunately, cases of infection have emerged, but we have to the extent possible taken appropriate steps to prevent serious cases," Kato said in a report by state broadcaster NHK.
With China's Hubei province, home to some 60 million people, in virtual lockdown, strict limits on movement in several major Chinese cities, and bans on travel to and from the mainland, economists expect the world's second-biggest economy to take a short-term hit from the epidemic.
Financial leaders of the world's 20 largest economies (G20) said the coronavirus epidemic was a downside risk for the global economy, according to a draft communique prepared for a meeting on February 22-23.
Australia's Qantas Airways Ltd said on Thursday it will ground the equivalent of 18 planes, freeze recruitment and ask its 30,000 staff to use up annual leave as it grapples with falling demand in Asia due to the epidemic.
About 80% of scheduled airline capacity to, from and within China has been cut this week, with Chinese airlines the hardest hit.