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Minister of Health Jane Philpott speaks to reporters following a caucus meeting on Parliament Hill in Ottawa on Wednesday, Nov. 23, 2016.Sean Kilpatrick/The Canadian Press

In a bid to crack down on private payments in Canada's health-care system, Ottawa is asking Saskatchewan to end a program that allows for-profit clinics to charge for MRI scans so long as those clinics provide an equal number of free scans to people on the public waiting list.

Federal Health Minister Jane Philpott sent a letter to her Saskatchewan counterpart earlier this month expressing her "significant concerns" that the two-for-one magnetic resonance imaging program "runs counter to the fundamental principle" of the Canada Health Act, the federal legislation that is supposed to protect Canadians from paying out-of-pocket for medically necessary care.

Although Dr. Philpott said she would prefer not to cut health transfers to the Prairie province, she left that possibility open after Saskatchewan Health Minister Jim Reiter said he had no intention of scrapping legislation that has shortened waiting lists and saved more than a million dollars since it took effect at the end of February.

"We've alleviated pressure in the public system at no cost to taxpayers," Mr. Reiter said. "So we think it's the right thing to do and we plan to continue with it."

Dr. Philpott's letter to Saskatchewan is the latest evidence that the Trudeau government is serious about taking on provinces that flout the Canada Health Act – a change from previous governments that is heartening to supporters of medicare, but discouraging to those who think the system would benefit from more private options.

In September, Dr. Philpott sent a letter to Quebec threatening to claw back transfer payments if the province did not bar doctors from charging extra fees for medically necessary care. Quebec agreed to halt extra billing beginning in January.

Dr. Philpott has also asked Health Canada to contact any other province that allows out-of-pocket payments for diagnostic scans to reiterate the federal position on the issue.

"This is very different from the benign, and sometimes not so benign, neglect, of previous governments," said Ryan Meili, a member of the board of Canadian Doctors for Medicare and a Saskatoon family doctor. "I think it means we've got a health minister who's really committed to medicare."

The Canada Health Act gives Ottawa the power to dock provinces on a dollar-for-dollar basis if they permit violations of the Act, but past federal governments have been reluctant to use it.

British Columbia was the only province to have its transfer cut in 2014-15, the most recent year for which figures are available. The province lost $241,637 in federal funding because of extra billing and user fees charged at private clinics in 2012-13.

In the last two decades, Ottawa has cut just over $10-million in transfers to provinces that violate the Canada Health Act, a tiny fraction of the billions the federal government sends to provincial governments for health costs. (The Canada Health Transfer is expected to top $36-billion in 2016-17 alone.)

Saskatchewan is one of five provinces that have never been penalized for violating the Canada Health Act.

The province's MRI Facilities Licensing Act allows private clinics to charge individual patients or third-party organizations – including the Workers' Compensation Board and the Saskatchewan Roughriders football team – for their scans. The two private clinics in Regina that have joined the program then have to provide a free scan of equal diagnostic complexity to a patient on the public waiting list within 14 days.

The cost of an MRI scan varies and the government is not tracking what the private clinics charge, according to a spokeswoman for the Saskatchewan Health Minister. The legislation does not limit the fee.

The program has led to more than 2,200 MRI scans in nine months at no cost to the public purse. The waiting list for MRIs was 700 patients shorter in the most recent three-month update than it was the three months before.

Bacchus Barua, senior economist for health-care studies with the Fraser Institute, a think tank that favours more private options in medicare, said the program is another example of how successfully Saskatchewan has tackled waiting times.

"If there's any province that we (or Minister Philpott, in this case) should be looking at for lessons on how to reduce wait times, it's probably Saskatchewan," he said by e-mail.

Saskatchewan is planning to expand the two-for-one program to cover CT scans next year.

"The federal government has told us for a long time to be innovative in health-care delivery," Mr. Reiter told reporters Monday. "We think that's what we're doing."

Dr. Philpott disagreed. Saskatchewan's approach is "bad policy" that allows the well-off to buy their way to the front of the queue, she told reporters in Ottawa.

"The fact that they brought their waiting list under control [proves] that they have the capacity to deliver the care, but those people already paid for that care through their taxes. They shouldn't have to pay again," she said.

With a report from Laura Stone