"Telling kids to not smoke pot is not a partisan attack on Justin Trudeau by Health Canada," Ambrose told a news conference Monday on the sidelines of the annual Canadian Medical Association meeting.
"It is a sound public health policy backed by science. Whether pot is legal or illegal, the health risks of marijuana to youth remain the same, and we should all be concerned about them."
She added that Trudeau "made this a political issue."
The Liberal leader lashed out at Conservatives last week over reports that Health Canada has approached three doctors' groups to sign onto an anti-pot advertising campaign directed at youth. All three have declined to participate, saying the campaign has become a "political football."
Trudeau suggested the move was meant as an attack on him and his support for legalizing marijuana. The proposed campaign came on the heels of several Conservative cabinet ministers, including Peter MacKay and Julian Fantino, publicly maligning Trudeau's stance.
"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."
Ambrose denied the government was focusing on marijuana rather than alcohol, which studies have shown pose greater dangers to young Canadians.
"There are a lot of campaigns on substance abuse... whether it's alcohol or drugs," she said. "These are all areas of public health concerns that Health Canada and public health agencies have long worked on and will continue to work on."
Earlier Monday, Ambrose delivered a speech to the CMA that focused on a wide range of public health concerns, including seniors care and efforts to crack down on opioid abuse.
She announced that the federal government is putting stronger warning labels on extended-release painkillers like OxyContin in an effort to prevent the abuse of opioids.
"Too many people are abusing prescription drugs," Ambrose said. "Too many people are suffering and dying as a result."
The Conservatives' new initiatives include stronger warnings on opioid labels that emphasize the risks and safety concerns associated with the drugs. The new labels also remove reference to "moderate" pain to clarify opioids should only be used to manage severe pain.
Canada is the second-largest per capita consumer of prescription opioids in the world, behind the United States.
A 2012 study suggests that close to a million young Canadians between the ages of 15 and 24 reported using prescription drugs in the previous 12 months.
The Canadian Alcohol and Drug Use Monitoring Survey also found that 410,000 Canadians said they'd abused prescription drugs like opioid pain relievers, including Demorol and OxyContin; stimulants like Ritalin and Adderall; and tranquilizers and sedatives that include Valium, Ativan and Xanax.
A year ago, the U.S. Food and Drug Administration announced safety labelling changes for all extended-release and long-acting opioids intended to treat pain.
David Juurlink, a medical toxicologist at the University of Toronto, said it's "hard to argue" with label changes but added OxyContin and related drugs should have been restricted to patients in severe pain as soon as they came onto the market.
"It's not likely to change how doctors prescribe opioids," he said in an interview. "That horse has bolted."
Ottawa needs to go much further, Juurlink added.
"What we really need are federal initiatives to quantify the toll of opioid misuse, to properly educate doctors about the risk/benefit profile of opioids and perhaps even federal support for an investigation into how these drugs were marketed in Canada," he said.
"That's happening in the United States, and for good reason. Why it's not happening here, I don't know."
Ambrose denied the measures lacked clout.
"Yes, we have work to do with the prescribing community," she said. "Maybe it won't stop a doctor from prescribing an opioid, but perhaps someone might read that label and think: 'Well I don't have severe pain, why am I being prescribed this?'"
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