Health Canada says Tilray, a Nanaimo supplier, is telling clients to stop using its Sativa House Blend, Hybrid House Blend and Indica House Blend.
The pot was contaminated with enterobacter, which is not associated with an acute health risk, said Joshua Eades, Tilray's chief science officer.
He said the company doesn't know where the bacteria originated.
"We are undergoing a top-to-bottom, rigorous review of our sanitation practices and procedures," he said. "And we'll be doing a root-cause analysis to understand what caused these results."
Health Canada and Tilray say there have been no reports of adverse reactions.
The law governing the production of medical marijuana says it must be manufactured to the same standards as any medicine.
This is the third recall of medical marijuana in the past year.
Last April, another Nanaimo company, Greenleaf Medicinals, recalled one of its products because of unspecified issues with its production. Last month, an Ontario company recalled some product because it was stronger than its label indicated.
Health Canada spokesman Sean Upton said in an emailed statement that microbial and chemical contaminants of dried marijuana must be within generally accepted tolerance limits referred to in the Food and Drugs Act.
"Licensed producers must maintain consistent specifications for their products and assess each lot or batch of dried marijuana against those specifications before approving the release of a lot or batch for sale," he added.
He said licenced producers must maintain records summarizing the testing protocols they followed and details of testing results for each batch or lot of finished dried marijuana.
Eades said the Health Canada inspections take place monthly.
"Health Canada sets very stringent quality control standards," he said. "We test every batch that's produced."
Eades said between 300 and 400 people have been affected by the recall and the company has contacted 90 per cent of them.
Tilray is telling clients to destroy the recalled product by mixing it with water, then cat litter or coffee grounds, and then to dispose of it with household garbage.
The company will give clients a credit for replacement costs.
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