Team Garmin-Sharp told CBC Sports Hesjedal is in hospital where he is being evaluated by hospital and team medical staff.
Hesjedal, 32, had been in second place after the first two stages.
It's another blow for the Victoria native. The champion at the 2012 Giro d'Italia, he was unable to complete the competition this year, suffering an upper respiratory tract infection during the last month.
He pulled out before the 11th stage.
The Tour du France, the sport's showcase event, is set to begin June 29.
More to come