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Former minister of Veterans Affairs Jody Wilson-Raybould, left, is pictured with former president of the Treasury Board Jane Philpott at a news conference in Ottawa, on April 13, 2017.Chris Wattie/Reuters

Jane Philpott stuck her neck out shortly after Jody Wilson-Raybould resigned as minister of Veterans Affairs on Feb. 12, tweeting out a picture of the two friends on a fishing boat when they were both members of the Liberal cabinet.

“You taught me so much − particularly about Indigenous history, rights and justice,” Ms. Philpott said on the social-media platform, pointing to major bills the two had worked on. “I know you will continue to serve Canadians.”

The pair had quickly developed a strong friendship after the 2015 election, dining out together in Ottawa when they were both ministers. Last week, Ms. Philpott said they stayed in touch as Ms. Wilson-Raybould was getting ready to speak to the justice committee of the House.

But after Ms. Philpott quit as president of the Treasury Board on Monday, it became clear that her message three weeks ago had also been a warning to her government. Not only was Ms. Philpott displeased with the handling of the SNC-Lavalin controversy, she was also willing to put her entire political capital in defence of Ms. Wilson-Raybould, who said last week that she endured inappropriate political pressure on the file.

“I must abide by my core values, my ethical responsibilities, constitutional obligations. There can be a cost to acting on one’s principles, but there is a bigger cost to abandoning them,” she said.

The news of Ms. Philpott’s departure from cabinet was stunning both because she was seen as one of the most competent ministers in Ottawa, but also because she possesses a strong reputation for integrity on Parliament Hill and across the country.

A medical doctor who lost a young daughter to meningococcemia in Africa in 1991, Ms. Philpott quickly turned heads in Ottawa after entering Justin Trudeau’s cabinet as minister of health in 2015. At ease in front of the cameras and known for her firm grip of a large number of files, she earned positive reviews for her work on contentious issues such as medically assisted suicide and the legalization of cannabis.

In 2017, she was shuffled to Indigenous Services where she won widespread support for her efforts to improve the lives of aboriginal Canadians, including efforts to bring down the number of boil-water advisories on reserves.

Assembly of First Nations national chief Perry Bellegarde described Ms. Philpott’s resignation as “a major loss” on Monday. In a statement, he said they worked together on many files, including child welfare, improving drinking water and improving the quality of life for First Nations.

“She acts with integrity, honesty and commitment in all her efforts,” he said.

Ms. Philpott took over at Treasury Board in the same Jan. 14 cabinet shuffle that saw Ms. Wilson-Raybould shuffled from Justice to Veterans Affairs. At the time, Prime Minister Justin Trudeau said that Ms. Philpott was a “natural choice” for the crucial portfolio at the heart of financial decisions in Ottawa, cementing her reputation as a key cog in the Liberal government.

Her resignation now raises questions about Mr. Trudeau’s ability to successfully manage the SNC-Lavalin controversy and to be able to put a positive spin on the budget that will be tabled on March 19. In announcing her decision to quit cabinet, Ms. Philpott said the decision was painful but necessary.

Ms. Wilson-Raybould responded by calling her friend a “mother of country.”

“For almost 4 years, our country has witnessed your constant & unassailable commitment to always doing what is right & best for Cdns. You are a leader of vision & strength & I look forward to continuing to work alongside you,” Ms. Wilson-Raybould said on Twitter.

Indigenous leaders praised Ms. Philpott for her commitment to issues confronting First Nation, Métis and Inuk peoples, whether in her role as minister of health or as minister responsible for Indigenous services.

Grand Chief Alvin Fiddler, of the Nishnawbe Aski Nation (NAN) in northern Ontario, called Ms. Philpott a “rare breed of minister” and an “ally” to Indigenous peoples, citing her work on issues such as health care, infrastructure, water quality and child-welfare services.

“She was hands-on with her work, taking the time to travel extensively − not just to NAN, but to other parts of the country − to see firsthand the conditions and to build the relationships that are so critical to making progress,” he said.

While he is “not 100-per-cent happy” with the child-welfare legislation introduced last week, he appreciated Ms. Philpott’s devotion to that file while Indigenous services minister and is hopeful that there will be positive amendments.

Grand Chief Ed John, who is serving his 11th consecutive term as an elected leader on the B.C. First Nations Summit, said he has dealt with multiple ministers over the years and was particularly impressed by Ms. Philpott.

“She came absolutely prepared to sit and talk and understand the issues in a way I hadn’t seen,” he said. “She was also responsive. She didn’t wait until next week. She acted on things as they arose.”

He said that if the Prime Minister is dedicated to reconciliation, he must “double down” and act on issues of importance to Indigenous communities. “The government is in a bit of a confidence crisis, and within this atmosphere, the commitments that have been made need to be honoured,” he said.

Ms. Philpott’s responsibilities are currently being taken over by Carla Qualtrough, who will continue to act as Minister of Public Services and Procurement. One of the main responsibilities at Treasury Board is to manage the government’s expenses, particularly the more than $45-billion spent annually on personnel costs.

Ms. Philpott was in the midst of collective bargaining with more than 100,000 public servants represented by the Public Service Alliance of Canada, the largest union of federal employees.

“We share the shock of thousands of PSAC members across the country at the news of Minister Philpott’s resignation,” said PSAC President Chris Aylward in a statement. “Despite the broader implications of her resignation from cabinet, there is a direct concern for over 100,000 of our hardworking members who are currently at the bargaining table with Treasury Board.”

Mr. Aylward had recently expressed some optimism that Ms. Philpott had shown some “modest movement” at the negotiating table.

The Treasury Board president is responsible for introducing the annual spending estimates in Parliament. Treasury Board and the Finance Department have been working on a major overhaul of the system so that the estimates line up with measures that are announced in the budget. The plan is meant to improve transparency, but an interim step adopted last year led to criticism that Ottawa had created a $7-billion “slush fund” that weakened Parliament’s control over federal spending.