The Transportation Safety Board confirmed that at 07:30 EST (12:30 GMT), a Porter Airlines flight from Ottawa to Toronto nearly collided with what they believe was a drone.
Two crew members received minor injuries during the manoeuvre.
Investigators at Billy Bishop Airport are looking into the incident.
The flight was at an altitude of approximately 9,000ft (2,740m) over Lake Ontario and making its initial approach for landing at Toronto's island airport on Monday when the pilots noticed an object in the distance.
As they got closer the pilots realised the object, which they first believed was a balloon, was very close to the flight path. They decided to take evasive action.
Porter is working with the Transportation Safety Board investigators, according to a statement.
The injured flight attendants were taken to hospital and have since been released. The 54 passengers on the flight were unharmed.
Transport Canada and the Federal Aviation Authority in the US both have "No Drone Zone" safety campaigns meant to highlight the dangers of flying drones near airports and other areas that could put aviation safety at risk.
Canada's transportation safety authority is investigating after an aeroplane had to take evasive action to avoid a near mid-air collision.