Several Canadians also traveled on a U.S. plane that had empty seats and was scheduled to depart shortly after the Canadian plane.
The federal government was also facing questions over how it planned to get other Canadians out of the quarantined city, even as it announced having secured several dozen additional seats on board a USA -chartered aircraft.
Dozens of Canadians also left China on board a United States government flight that left a few hours after the Canadian flight.
Anyone who is ill will not be allowed to board any of the repatriation flights, and Hajdu said passengers will also be assessed by Department of National Defence.
Canadian military personnel talk near makeshift tents set up in front of the Yukon Lodge where passengers from an airplane carrying Canadian citizens flown out from the coronavirus zone in Wuhan, China, are staying at CFB Trenton in Trenton, Ontario, Canada on February 7, 2020.
"The plane is wheels up", Foreign Affairs Minister Francois-Philippe Champagne said in a tweet Thursday afternoon after the evacuation flight organized by the federal government departed from Wuhan, the city in central China where the outbreak originated.
Champagne said Canadians in China, but outside of the quarantine area should leave on commercial flights if possible.
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Meanwhile, all Canadians are asked to avoid all non-essential travel to China, and all travel to the Hubei province.
"I think it's a good thing because everybody who wants to depart will have a third chance to come back to Canada", Champagne said at a news conference Thursday in Ottawa.
Champagne noted "a small number of no-shows" at the Wuhan airport who had "changed their minds at the last minute".
Passengers told local media that most slept through the long flight.
The federal government is awaiting final approval from the Chinese government to fly through the restricted airspace and land at the closed airport in Wuhan, but Champagne said other preparations are already well underway.
The company said the Canadians were among 41 positive tests for the virus identified in the latest round of tests conducted by the Japanese Ministry of Health.
The ship with 2,666 guests and 1,045 crew members was quarantined for the first time on Tuesday in Yokohama after a confirmed outbreak of the new corona virus.
That city, with a population of 11 million people, has been under heavy lockdown by the Chinese government in an effort to contain the spread of the virus.