Transportation Minister Lisa Raitt's emergency directive was mandatory and effective immediately, she said.
"If you're carrying passengers, this is going to apply to you," she said yesterday outside the House of Commons.
"You have to have two crew members in the flight deck at all times."
Raitt explained that the second person could be a flight attendant if the pilot or co-pilot has to exit the cockpit in flight.
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Canada's flagship carrier Air Canada, Westjet and charter airline Air Transat were among the airlines that confirmed the policy change to AFP.
Earlier, French authorities said the co-pilot of the Germanwings flight appeared to have slammed his Airbus A320 into the French Alps, killing all 150 passengers and crew.
The 28-year-old initiated the plane's descent while alone at the controls and refused to open the locked cockpit door for the captain, who was believed to have gone to the toilet.