The driver of the bus was arrested at the scene, Chief Charles Bordeleau of the Ottawa police added at an evening news conference at Ottawa city hall.
The accident happened at 3:50 p.m. local time on Friday when the second floor of the bus struck the roof of the Westboro bus station, which is located in the city's Westboro neighborhood.
Three people were killed and almost two dozen injured in a collision involving an OC Transpo double-decker bus at Westboro station Friday afternoon. Their names have not been released.
Scott Street and the Transitway were closed between Westboro station and Tunney's Pasture.
Buses are being detoured as a result of the crash, OC Transpo said. Bordeleau said the Ottawa Paramedic Service and Ottawa Fire Services worked the scene in partnership with the Ottawa Police.
"Our hearts and condolences go out to all those injured [and] those family members who have lost loved ones", Watson said.
Ottawa Police said in a statement its collision investigation unit was on scene and is investigating.
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"This will be a long investigation", Bordeleau said.
Investigators were expected to be on the scene through the night, with frigid temperatures in Ottawa expected to dip down to minus 22 degrees Celsius overnight.
Officials from Transport Canada and Ontario's Ministry of Transportation are also investigating.
OC Transpo's latest performance report covering January to June 2018 showed that 269 buses mostly hit their stops on time, though less often than most other "Connexion" routes, which operate only during weekday rush hours.
Bilal Gill, a passenger on the upper deck, told broadcaster CBC News that people at the front were pinned under their seats. "There was definitely people pinned".
OC Transpo general manager John Manconi told reporters the bus could have been holding as many as 90 passengers and that the agency would be co-operating fully with the investigation.