During a visit to Saskatoon, he suggested the move is meant as an attack on him and his support for legalizing marijuana.
"We know that Canadian taxpayers are getting extremely frustrated with the fact this government tends to use public money for ads that do more for its partisan aims than for actual public service," Trudeau said.
"It's a real concern that this government has its priorities in the wrong place."
The Postmedia report said Health Canada has approached the Canadian Medical Association, the Royal College of Physicians and Surgeons of Canada and the College of Family Physicians of Canada.
The report quoted an unnamed source as saying the organizations wouldn't have to pay for the $5 million campaign, but their logos and endorsements would appear in them.
A spokeswoman for federal Health Minister Rona Ambrose said Thursday there is "nothing political about ensuring parents and youth know the dangers of using drugs."
"I'd encourage Justin Trudeau to support any campaign on educating parents and youth on the harmful effects of marijuana," Cailin Rodgers said in an email to The Canadian Press. "Justin Trudeau can stand for pot but we are standing up for parents who want to know the harmful effects of marijuana on their kids.
"This is about public health, not politics."
Trudeau said he agrees with Health Canada's message that marijuana use in young Canadians is dangerously high, but said the government shouldn't pay for what he calls partisan ads.
He said Canadians want a debate based on logic and evidence when it comes to marijuana laws in the country.
Current marijuana laws are failing to protect teens from the dangers of the drug and are fuelling criminal enterprises by keeping it illegal, he said.
Trudeau said he is not advocating making pot available for young people but rather opening up discussion on how to make the current laws more effective.
(CKOM, CKRM, The Canadian Press)