The company did not say when the flight would take place other than that it would be in "the coming weeks."
The first flight of the CSeries has been delayed several times.
It was initially expected to fly by the end of 2012, but that was delayed until June, then to the end of July and recently for a "few weeks" more.
Bombardier said the flight test permit follows a series of pre-flight tests including low-speed taxi runs.
The test aircraft will now start high-speed taxi runs to simulate the speeds for take-off.
"Five years in the making and, today, following receipt of Transport Canada's flight test permit, we are very close to the CSeries airliner's first flight," said Mike Arcamone, president of Bombardier Commercial Aircraft.
"The CSeries aircraft teams have spent the last few weeks completing rigorous exercises to ensure the integrity and maturity of the aircraft are absolutely in check with the flight crew's requirements."
RBC Capital Markets analyst Walter Spacklin noted the announcement reinforced guidance provided by the company during a recent conference call.
"As a result, we view this news favourably as it suggests that further delays to this key milestone in the CSeries' development is less likely at this point,"
The CSeries jet is expected to compete with some of the smaller planes made by Boeing and Airbus.
It represents a significant step forward for the company better known for its business jets and regional aircraft.
The plan uses advanced composite materials in its construction to reduce weight and new engines that are expected to be quieter and more fuel efficient.
Bombardier has received 388 commitments for the aircraft, including 177 firm orders as of June 30.