Team doctors say Mainguy, from Quebec City, injured herself in a fall while training.
"She suffered a concussion and collar bone fracture," team doctor Susan Labrecque said in a release. "The collar bone fracture prevents her from moving her left arm, therefore she can't hold her handlebar securely."
The time trials for all para-cycling events are scheduled for Tuesday.
"Receiving the news about my withdrawing was like a slap in the face," Mainguy said in a statement. "I did not want to believe it, I wanted to keep training. I am really, really disappointed."