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.

Another 11 were injured when the driver lost control of the minibus and ploughed through a crash barrier.
Local media said no foreign tourists were among the passengers.
Turkish media said the vehicle was heading towards Marmaris for a mother's day event, which is celebrated on Sunday there.
The victims are believed to be mainly women and children.
Amric Cicek, governor of Mugla province, suggested the brakes may have stopped working.
But the mayor of Marmaris, Ali Acar, told Turkish newspaper Hurriyet: "I think that the accident was a result of driver error."
Turkey's Andalou news agency said the crash took place on the Mugla-Antalya road at the Sakar Gecidi pass.
The vehicle landed on another section of road below after it went through the crash barrier.
Rescue teams were dispatched and the injured were taken to hospital, Andalou said.

Trainers contributed £98.6m and stud farms £81.2m, while visitors bring in £8.8m to the racecourses.
Forest Heath District Council commissioned research company SQW to carry out the study into the impact of the sport on the 'Home of Horseracing'.
The SQW report did not try to measure the amount spent by owners and visitors at local shops and on services.
The council said the survey, commissioned along with the Newmarket Horsemen's Group (NHG), aimed to "understand the scale and economic significance" of the industry.
SQW report
William Gittus, chairman of the NHG, said: "It's a global industry and we are keen to attract global investors and to develop planning and economic policy.
"We who work in the industry know it's very valuable to the local economy, but we needed to provide concrete evidence to people who make those policy decisions."
Councillor James Waters, Conservative leader of the the Council, said: "We have never before had an independent, fact-based report on exactly what impact the horse racing industry has on Newmarket.
"It looks at the impact of racing up to 25 miles away, so will be a really useful document as we plan future growth in west Suffolk."
The survey did not attempt to calculate how much visitors or people in the racing industry spent in the town centre.
Trainer John Gosden said: "Obviously the report has been very careful to never have any figures challenged and I think they've underestimated the financial contribution to the region, but they didn't have access to people's private accounts.
"What we have had here in the last 15 years is an incredible investment from the Middle East and Far East."
Kevin Pearson, from Golding clothing shop and a member of the Newmarket Retailers Association, said: "The majority of horse owners and training staff do shop locally and this adds to the vibrancy of the high street."
Canada's transportation safety authority is investigating after an aeroplane had to take evasive action to avoid a near mid-air collision.
[NEXT_CONCEPT]
At least 23 people have died after a tourist bus fell from a cliff near the southern Turkey seaside resort of Marmaris.
[NEXT_CONCEPT]
The horse racing industry is worth £208m a year to the economy in and around Newmarket, a study has revealed.