The man, who was a Hong Kong resident, died on 6 March, according to the public broadcaster NHK. It is not yet clear whether he was a passenger or a crew member.
The ship with over 3,700 people on board was quarantined off the Japanese city of Yokohama in February after a passenger who came off it in Hong Kong tested positive for the virus.
Japan has confirmed more than 1,100 cases of infection with the COVID-19 disease, more than half of them from the virus-stricken ship.
The number of confirmed coronavirus infections globally has surpassed 102,000, with almost 3,500 deaths, a vast majority of which were in China’s Hubei province where the virus originated. At the same time, more than 57,000 people have recovered.