The ministry said 79 new cases were confirmed, adding that 68 of the people were said to be asymptomatic.
The cases were taken from 607 samples on the cruise ship that has been docked in the Japanese port of Yokohama for two weeks.
In Japan, a total of 692 novel coronavirus cases have been confirmed, with 624 from the Diamond Princess and 68 outside the ship.
Roughly 800 passengers disembarked the vessel on Wednesday, Japanese health ministry officials told CNN. The official did not give the exact number.
Before the disembarkation, there were about 3,100 passengers and crew on board on Wednesday morning.
Among the remaining passengers are citizens of Canada, Australia, Italy and other nationalities who are due to fly back on chartered flights.
More than 300 Americans were evacuated over the weekend and are now in quarantine at two US bases.
Written by journalist Akanksha Sharma in Hong Kong.