The plane had just left Halifax Stanfield International Airport and reached an altitude of 6,000 metres when the pilot spotted an "unmanned aerial vehicle" 300 metres above the plane.
Transport Canada spokesman Martin Eley said most drones are unable to reach that kind of altitude, which could make it easier to identify.
Eley said there wasn't risk to the people on the flight in this incident, but educating people about safely operating drones is vital.
"You get two things in the air, there's obviously a risk. Our job is to make sure we do keep things safe, we avoid the risks. The pilot reported seeing it, he didn't indicate that he may have hit it, he might have taken evasive action," he said.
Eley said it's not clear what would have happened had the plane and drone collided.
"We haven't done specifically testing with drones, but certainly aircraft, when they're certified to be capable of withstanding a hit from particularly wildlife, birds primarily, fairly large birds, that's part of the testing, but it depends very much on what part of the aircraft — there's a lot of variables in there," said Eley.
"The aircraft are tolerant, but obviously it's hard to say about a particular aircraft."
Eley said it's not clear where the drone came from, but an investigation is underway.
Recreational drone users don't need approval from Transport Canada, but commercial and other non-recreational users do.
Eley said Transport Canada is working on an education campaign to make users aware of the risks and responsibilities of flying drones.