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Justin Trudeau and Jody Wilson-Raybould take part in the grand entrance as the final report of the Truth and Reconciliation commission is released in December of 2015.

Adrian Wyld/The Canadian Press

Jody Wilson-Raybould resigned from Justin Trudeau’s cabinet on Tuesday in a departure that fuels a growing political controversy over allegations that the Prime Minister’s Office put pressure on her while she was justice minister and attorney-general to shelve a corruption and fraud prosecution of Montreal construction giant SNC-Lavalin Group Inc.

The Prime Minister said he was surprised, disappointed and puzzled by her sudden resignation, one day after he said Ms. Wilson-Raybould’s continued presence in cabinet was an indication she was not unhappy with the government.

On Monday, Mr. Trudeau said, “Her presence in cabinet should actually speak for itself.” Hours later, Ms. Wilson-Raybould told him she was resigning.

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The Globe and Mail reported last week that Ms. Wilson-Raybould had come under pressure from the Prime Minister’s Office to override the decision of the Public Prosecution Service of Canada and shelve a criminal prosecution of SNC-Lavalin in favour of a negotiated settlement – a remediation agreement – without a trial. The company faces charges of bribing Libyan officials between 2001 and 2011 in exchange for contracts. SNC-Lavalin is seeking a judicial review of the director of public prosecutions’ decision.

Prime minister Justin Trudeau says he was surprised and disappointed by Jody Wilson-Raybould’s resignation Tuesday. The Canadian Press

At an evening news conference in Winnipeg, Mr. Trudeau repeatedly stated that Ms. Wilson-Raybould had never complained to him about political pressure from his office.

“I, to be honest, don’t entirely understand why Jody Wilson-Raybould made the decision she did, because if anyone, particularly the attorney-general, felt that we were not doing our job responsibly and according to all the rules as a government, it was her responsibility to come forward to me this past fall and highlight that directly to me,” Mr. Trudeau said. “She did not. Nobody did and that is why I continue to be puzzled.”

However, senior government officials told The Globe in recent days there was vigorous debate among Mr. Trudeau’s staff and other government officials, including cabinet ministers, involving Ms. Wilson-Raybould, over the SNC-Lavalin prosecution, but they argued it should not be construed as pressure. The officials said the government was concerned about the impact of a conviction on the company and its employees.

Read Jody Wilson-Raybould’s resignation letter to Justin Trudeau

Updates: SNC-Lavalin, Jody Wilson-Raybould and Trudeau’s PMO: The story so far

The exit of an accomplished Indigenous woman from the cabinet drew expressions of support for the former minister from Indigenous leaders, who also voiced concern that her departure is a blow to Mr. Trudeau’s election promise to repair relations with First Nations.

“With a heavy heart, I am writing to tender my resignation as the Minister of Veterans Affairs and Associate Minister of National Defence,” Ms. Wilson-Raybould told the Prime Minister in a resignation letter that she made public.

Ms. Wilson-Raybould, a former Crown prosecutor and Indigenous leader who was a star candidate for the Liberals in the 2015 election, wrote that she had entered public life because she believed in a different way “of doing politics.”

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In her letter, Ms. Wilson-Raybould said she cannot discuss what has transpired since The Globe broke the allegations, but indicated she would like to tell her side of the story.

She is bound by solicitor-client privilege and cabinet confidentiality, but has hired former Supreme Court Justice Thomas Cromwell to guide her on what she might be able to reveal.

“I am aware that many Canadians wish for me to speak on matters that have been in the media over the last week,” she wrote. “I am in the process of obtaining advice on the topics that I am legally permitted to discuss in this matter and as such have retained the Hon. Thomas Albert Cromwell ... as legal counsel.”

Related: Wilson-Raybould retains former Supreme Court justice to advise her on what she can tell public

On Monday, Mr. Trudeau said he has asked Justice Minister David Lametti to examine whether to waive solicitor-client privilege. On Tuesday, he cautioned that he had received some advice against doing this.

“I will highlight, however, that there has been a real danger that has been flagged for me of unintended consequences particularly because there are two court cases ongoing directly related to this matter that could be impacted by such a decision we might make,” Mr. Trudeau said.

Ms. Wilson-Raybould informed Mr. Trudeau on Monday night of her resignation, and he told cabinet on Tuesday morning of her departure. Defence Minister Harjit Sajjan has taken over as acting Minister of Veterans Affairs for the time being.

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“This resignation is not consistent with conversations I had with Jody a few weeks ago when I asked her to serve as Canada’s minister of veterans affairs and associate minister of national defence nor is it consistent with the conversations we had lately,” Mr. Trudeau said, without indicating what the exchanges were about. “With regard to SNC-Lavalin, let me be direct the government of Canada did its job and to the clear public standards expected of it.”

The 47-year-old British Columbian said she will continue to serve as Member of Parliament for Vancouver-Granville. A source close to the former minister said this was a really awful day for her and for her supporters, who consider her to be a person of high integrity.

Globe editorial: On SNC-Lavalin, Justin Trudeau’s silence isn’t going to help

Opinion: Wilson-Raybould’s departure is a calamity for Trudeau’s Liberals

SNC-Lavalin scandal exposes flaws in Canada’s anti-corruption defences

Ms. Wilson-Raybould was appointed as Canada’s first Indigenous justice minister in 2015. Last month, Mr. Trudeau shuffled her to the veterans portfolio, replacing her with Mr. Lametti, a Montreal MP. Mr. Lametti has not ruled out staying the prosecution of SNC-Lavalin.

On Monday, the federal Ethics Commissioner has launched an investigation into the matter.

Ethics Commissioner Mario Dion told the NDP earlier this week that there is enough evidence to warrant an investigation under the Conflict of Interest Act.

Mr. Trudeau told journalists in Vancouver on Monday he had gone back to Ms. Wilson-Raybould and sought verification that he had not directed her to abandon the SNC-Lavalin prosecution.

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"She confirmed for me a conversation we had this fall where I told her directly that any decisions on matters involving the director of public prosecutions were hers alone," Mr. Trudeau said.

Mr. Trudeau’s communications director, Cameron Ahmad, said on Tuesday that Mr. Trudeau had that discussion with Ms. Wilson-Raybould on Sept. 17, before federal prosecutors decided on Oct. 10 to proceed with the case against SNC-Lavalin. Mr. Trudeau has said he never directed Ms. Wilson-Raybould to abandon the case.

Conservative Leader Andrew Scheer called on the Prime Minister to preserve all documents relating to the issue so the public might learn what transpired.

His request applies to records held by the former justice minister and senior PMO officials, including chief of staff Katie Telford, principal secretary Gerald Butts, Quebec adviser Mathieu Bouchard, and senior adviser Elder Marques.

Since the beginning of 2017, representatives of SNC-Lavalin met with government officials and parliamentarians more than 50 times on the topic of “justice” and “law enforcement," according to the federal lobbyists registry. This includes 14 visits with people in the PMO, included Gerald Butts, principal secretary to the Prime Minister, and Mathieu Bouchard, Mr. Trudeau’s senior adviser on Quebec – whom they met 12 times. Mr. Trudeau’s senior policy adviser, Elder Marques, also met with company representatives.

On December, 5, Mr. Butts also discussed SNC-Lavalin and the remediation agreement with Ms. Wilson-Raybould at the restaurant in Ottawa’s Chateau Laurier Hotel. Mr. Ahmad, speaking for the PMO, said Ms. Wilson-Raybould raised the issue with Mr. Butts and he advised her to talk to Privy Council Clerk Michael Wernick.

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NDP Leader Jagmeet Singh urged Mr. Trudeau to allow the Commons Justice committee to launch hearings into the matter. The Liberals hold the majority of seats on the committee, which will meet on Wednesday on the matter.

Mr. Trudeau said he would not interfere in the Justice committee’s deliberations and Anthony Housefather, the Liberal chair of the committee, said Tuesday that he would support a call for hearings into the matter to determine “whether a line was crossed.”

Indigenous leaders expressed disappointment at the sudden departure of Ms. Wilson-Raybould. Grand Chief Doug Kelly, President of the Stolo Tribal Council, said her 2015 appointment to cabinet was taken as a sign that “indigenous people will finally be recognized, respected and treated vastly differently by the government of Canada.” He said he has sent her a message expressing his affection and support. “When I say that, I am speaking for thousands of indigenous people in B.C. ... we love the fact that she’s able to speak truth to power.”

Assembly of First Nations national chief Perry Bellegarde said he’s worried about what has transpired. "I am concerned about the many unanswered questions about Jody Wilson-Raybould’s departure and this is echoed by many First Nations across the country.”

Bill Wilson, Kwakwaka’wakw hereditary chief and Ms. Wilson-Raybould’s father, said he was not surprised to see his daughter take a stand, as that is how she was raised. He credited her mother, whom he separated from when Ms. Wilson-Raybould was a child, and her paternal grandmother for shaping the person she has become.

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“The courage that she had to take on the man, and the establishment, is also costing her [a lot] in salary every year, plus all the perks that come with being a cabinet minister. For her to bite the bullet and do that, to me, is praiseworthy. I’m even more proud of her now than I was before.”

Kory Wilson echoed her father's sentiments, calling her sister a person of principal and integrity.

“I’m really proud of her, and not just now, but ever since she got into politics,” said Ms. Wilson, who is executive director of Indigenous Initiatives and Partnerships at BCIT.

Ms. Wilson, who is in regular contact with Ms. Wilson-Raybould, said her sister is doing fine and has the full support of the family.

“She will always be poised and professional and follow her heart and do what she believes is the right thing to do,” Ms. Wilson said. “She’s got a lot of people who love her, she knows who her family is, and we are supporting her.”​

With reports from Wendy Stueck and Andrea Woo in Vancouver.

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