The former cruise ship passengers will spend the next two weeks in a camp facility near the northern Australian city, Australian health officials said.
The new coronavirus that causes the COVID-19 illness infected more than 600 people on the Diamond Princess.
The ship had been docked at the port of Yokohama since early this month in a quarantine that was widely considered a failure. The quarantine ended Wednesday and about 500 passengers who tested negative for the virus left the ship.
The group of Australian evacuees was flown from Japan in the early hours of Thursday morning on a Qantas 747 chartered by the Australian government.
Not evacuated were 46 Australians from the Diamond Princess who tested positive for the coronavirus. They would be treated in the Japanese health system, Australian health officials said.
More than 200 people are already quarantined at the Howard Springs facility after being evacuated from Wuhan, the central Chinese city that is the epicenter of the viral outbreak. The new group will be kept separate from the Wuhan evacuees, who remain in good health, Di Stephens, acting chief health officer of the Northern Territory, of which Darwin is the capital, said before the flight left Japan.
"These people need to go into quarantine because we are not entirely convinced that the quarantine procedures on that ship were 100% effective," Stephens said. "They'll be completely separated at the facility, they'll have separate medical staff looking after them and separate support staff in that quarantine zone."