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Health Minister Jane Philpott answers a question during Question Period in the House of Commons in Ottawa on March 9, 2017.PATRICK DOYLE/The Canadian Press

The federal government's efforts to craft a new decade-long health-care accord by obtaining deals with individual provinces and territories are nearly complete now that the three big hold-outs – Ontario, Quebec and Alberta – have said yes to Ottawa's terms.

The announcement Friday, that those provinces had signed agreements after three months of backroom talks, leaves Manitoba as the lone jurisdiction that has yet to accept what the Liberal government has put on the table.

The fact that a health-care accord could be reached through consultation but without a first ministers' meeting, as had been demanded by the provinces, is a result of private negotiations conducted directly by federal Finance Minister Bill Morneau and Health Minister Jane Philpott, government officials said. Mr. Morneau used the relationships he built with his provincial colleagues during discussions about changes to the Canada Pension Plan to forge a consensus on health funding.

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"This is not about divide-and-conquer," Dr. Philpott told reporters when asked about the strategy of cutting unilateral agreements with successive jurisdictions after the provinces and territories rejected what her government offered in December. "It took some time for several provinces to reflect on this," she said, "and on reflection, as they've sort of looked at this and realized that, in fact, this will be extremely helpful, they have, in their own time, come to an agreement with us."

The deals bring an end to the 6-per-cent annual increases in the Canada Health Transfer (CHT) – the money that Ottawa transfers to provinces and territories to help pay for health care – that have been in place since 2004. The CHT will instead rise by 3 per cent annually, or by a three-year average of nominal GDP growth, whichever is higher.

In addition, the federal government will provide $11.5-billion over the next 10 years to pay for new investments in mental-health care and home care. In the coming weeks, the provinces and territories will develop performance indicators and methods for reporting how the funds will be spent.

"The fact we now have 12 provinces and territories who have signed onto our approach to health is a great victory for federalism and mostly for Canadians," Prime Minister Justin Trudeau said in Texas, where he was attending a global gathering of politicians and energy-sector executives.

Although Manitoba remains without an agreement, Dr. Philpott said she expected to reach a deal with that province in short order. "No doubt people of Manitoba are keen to have additional resources for these particular areas," she said.

Health-care costs across Canada have climbed by less than the rate of inflation since 2011, but the provinces balked at taking a steep cut in the increase to the CHT because, they argued, an aging population means they will be paying more in the future. They had asked for 5.2-per-cent increase in the CHT. But with their own budgets looming, they opted to accept Ottawa's offer.

In addition to the money that will flow to other provinces, Alberta will get $6-million from the federal government to deal with its urgent opioid crisis. "Alberta, like British Columbia, has been disproportionately affected by overdose deaths," Dr. Philpott said.

Quebec and Ontario had been harshly critical of the federal offer and, at various points, vowed to hold out for a better deal than the one tabled by Dr. Philpott and Mr. Morneau in December.

Ontario Health Minister Eric Hoskins was unavailable for comment on Friday but the province released a statement saying the new money will mean improved wait times for mental-health services for children and youth, as well as more home care for patients who do not need to be in a hospital.

In Quebec, Premier Philippe Couillard said he was pleased with the agreement, even if he would have preferred a national deal with all the provinces.

"I regret that they had this approach of dividing the agreement into individual deals for each province and territory," he said. "They chose instead to take a province-by-province approach. Fine. We maintained and watched out for our interests, and each province did the same thing."

He said the agreement maintained the principle of asymmetrical federalism that was negotiated in 2004 as part of a federal-provincial health agreement. That deal allows Quebec to invest the federal funds according to its own priorities.

"It's essential to preserve that asymmetry, and we were even able to improve on it," Mr. Couillard said.

Quebec's Finance Ministry said the province also came to an agreement with Ottawa to allow it to use federal infrastructure-development funds "to finance its priorities for direct services to families."

With reports from Shawn McCarthy in Houston, Texas, and Ingrid Peritz in Montreal