Ten people were arrested in the raids, police said, including veteran pro-cannabis activist Marc Emery.
Trudeau, who campaigned last year on a promise to end nearly a century of pot prohibition, warned that the government is still at least one year away from legalizing pot use.
"We haven't changed the legislation yet," Trudeau told reporters earlier in Montreal. "It is coming, but we're going to take the time to do it right."
Emery on Thursday however went ahead and opened in Montreal six boutiques of the Cannabis Culture franchise chain, which already exist in other cities.
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Police raided the stores at the end of the day as buyers braved frosty conditions to crowd into the boutiques to buy marijuana.
"The prime minister is a disgrace, as is the Mayor of Montreal, Denis Coderre," Emery cried out as he was being taken away by police.
Those arrested will face charges of drug trafficking and possession of items for trafficking purposes, the Montreal police department said.
Emery, the self-proclaimed "Prince of Pot," has been arrested multiple times.
He was even extradited to the United States in 2010 and served just under five years in prison for selling on his website and mailing more than four million marijuana seeds. He returned to Canada after his release in August 2014.
In cities across Canada in the last year, entrepreneurs have opened storefronts seeking to grab market share ahead of the promised legalization.
The dispensaries themselves claim to be operating in a "gray area" of the law. Many have been raided by police only to defiantly reopen days later.
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