The agency took the action against Apotex Pharmachem India, Apotex Research Private Ltd. and IPCA Laboratories.
Health Canada says it has "significant concerns" with the manner in which research data is collected and reported, raising serious doubts about quality and safety.
The agency says until it is satisfied that production processes at the three sites meet international standards, it will keep the products off the market.
Apotex says in a statement that the ban is unwarranted and that it is confident Health Canada will be satisfied as to the integrity and quality of Apotex products imported from the Indian facilities.
Apotex also notes that many of the raw materials that are purported to be covered by the Health Canada notice are manufactured at its plant in Brantford, Ont., not India.
"Apotex fully tests every raw material and finished product imported from its Indian sites," the company said Wednesday.
"The facilities were recently inspected and given clearance by Health Canada and another international regulatory agency in February and August 2014 and were found to be compliant," it said.
Health Canada has said there are "no specific safety issues" with products now on the market from those companies, nor has a recall been requested.
It said that consumers should not make any change to their medication without first consulting with a health-care professional.
Health Canada also said certain medically necessary products may be excluded from the ban on the condition they are tested by an independent third party.
A full list of the banned medications and ingredients has been posted on the Health Canada website.