According to a spokeswoman for the area's police force one of the planes "crashed on the roof of one of the stores" and "the other one on the asphalt of the parking lot", according to STV.
Police said each plane only had a pilot on board, both of whom were injured in Friday's crash.
One witness at the scene of the crash in the Quebec suburb of Saint-Bruno said they heard a "loud boom" before seeing "pieces of plane fall out of the sky".
Nheil Martinez, who works at the shopping centre and was outside having a cigarette when the planes collided, said: "I heard the motor so low to the ground and then a loud boom. Then we saw pieces of plane fall out of the sky everywhere."
Another witness Jonathan Vanasse, who was eating at a restaurant next to the crash site, said he ran outside when he heard the noise and saw the shredded metal remains of the aircraft which appeared to be leaking fuel.
The Transportation Safety Board of Canada are still investigating but have confirmed both planes were Cessna 152 aircrafts operated by Cargair - a pilot-training academy based in nearby Longueuil.