Police say they received an anonymous call at around 6 a.m., and the site manager ordered an evacuation.
This follows similar evacuations of the McGill University Hospital Centre construction site on May 10 and June 12, which both turned out to be false alarms.
The approximately 1500 site workers have been sent home and delivery trucks are being turned away at the site gate.
Investigators say they have not yet found any signs of suspicious objects but continue to search the site.
Construction workers across Quebec returned to job sites on July 2, after provincial legislation called an end to a two-week strike.
Watch a tour of the MUHC superhospital site: