In announcing the suspension on Monday, Health Canada cited "significant concerns with good manufacturing practices" that were identified during an inspection of the company's drug wholesaling activities.
A Health Canada spokesperson told CBC News the licence was pulled for what Canadadrugs.com wholesales to pharmacies, other distributors or wholesalers, not for its direct-to-consumer online sales.
Individuals can still order medication from Canadadrugs.com's website because it has a valid provincial licence to operate as a pharmacy, according to Health Canada.
The College of Pharmacists of Manitoba has separately licensed the company to "sell drugs authorized in Canada to consumers via the internet," the federal agency said in a news release.
Health Canada has notified the college about its inspection findings and the suspension of Canadadrugs.com's establishment licence.
A company must comply with good manufacturing practices under Food and Drug regulations to ensure medications sold in Canada are safe, effective and of high quality.