Medical marijuana is legal in Canada, but only licensed providers can sell it to people who have a doctor’s approval.
Police raided 43 Toronto shops on Thursday and made 90 arrests.
Raids come just as Prime Minister Justin Trudeau’s Liberal Government is poised to make marijuana legal to recreational users.
Protesters gathered outside police headquarters on Friday, calling the medical marijuana dispensaries essential.
People held signs reading “Save Our Dispensaries” and “Bad Laws, Bad Cops”.
Toronto police chief Mark Saunders was shouted down by protesters as he held a news conference addressing the storefront raids on Friday.
The crackdown was on stores that police believe are selling marijuana to recreational users.
There are 83 known unlicensed marijuana dispensaries in Toronto.
He said the raids, which collected 269 kilograms of dried marijuana and many edibles such as cookies and candies, came in response to “significant complaints” from community members.
The stores had been selling marijuana products with “inaccurate information” about the amount of THC they contain, he said, calling it a “genuine health concern”.
“It’s a danger that you don’t know where the [marijuana] is coming from,” he said.
Marijuana dispensaries are in nebulous legal territory because while medical marijuana is legal across Canada, authorities say only sellers licensed by Health Canada, which distribute products via mail, are legal.
“Knowingly selling without a license issued by Health Canada is unlawful, you can’t be doing it,” said Mr Saunders.
Mr Trudeau made marijuana legalisation a key campaign issue and the Canadian government has said it will introduce legislation next year that would make the sale of marijuana legal.
If marijuana made legal in Canada, it would become one of the largest Western countries to allow widespread use of the drug.
Protesters shouted to Mr Saunders questioning the raid considering the likelihood that marijuana will become legal.
Another protester shouted “Where are the victims?” and said the current medical marijuana programme was set up under Stephen Harper’s Conservative government and cannot meet the demands of medical marijuana users across Canada.
“I don’t want to disrupt anyone getting legal access to medical marijuana,” said Mr Saunders. “You keep asking questions, but you don’t really want answers.”
He said he thinks there is enough medical marijuana supply in the country and that the raids of the shops were “low-key”.