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“Government by cabinet is back,” Justin Trudeau promised on his sunny first day as Prime Minister in November, 2015. But Mr. Trudeau broke that promise. Instead, he allowed a close circle of unelected advisers to direct, control and even bully cabinet ministers and MPs alike. On Tuesday, the government paid the price. ​

Jody Wilson-Raybould’s resignation is a calamity for the Liberals. For one thing, she has made Mr. Trudeau look like a fool. Less than 24 hours earlier, he had expressed full confidence in the minister, saying “her presence in cabinet should actually speak for itself.” Her resignation hours later spoke louder.

For another, her departure is politically damaging. Past governments have been crippled by cabinet ministers who resigned in protest. Pierre Trudeau lost the next election after his finance minister, John Turner, quit over personal and policy disagreements. Brian Mulroney’s government was crippled by the defection of Lucien Bouchard after the collapse of the Meech Lake Accord.

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Ms. Wilson-Raybould’s resignation could be just as damaging. For one thing, her decision appears to confirm that officials in the Prime Minister’s Office put pressure on her to cut a deal with SNC-Lavalin, which faces corruption charges, and then removed her from the Justice portfolio when she refused. This from a government that trumpets its scrupulous observance of the rule of law.

The fact that she stood up to the Prime Minister’s advisers, and was punished for it, undermines Liberal claims that women are equal and respected within the government. The resignation of the first Indigenous person to serve as justice minister also tarnishes the government’s record on Indigenous issues.

And perhaps the saddest thing of all: The next Minister of Veterans Affairs will be the fourth appointed by this government, underscoring the low value placed on the portfolio, and on the needs of veterans.

Ms. Wilson-Raybould would certainly have been effective, had she remained in her new job. As justice minister, she implemented two of this government’s most important achievements: assisted-dying legislation, and the legalization of marijuana.

That such an accomplished minister no longer wishes to be in cabinet says much about Justin Trudeau’s leadership, and the acumen of his advisers.

We are only at the beginning of this affair. The reason for Ms. Wilson-Raybould’s resignation will crowd every other item off the political agenda for who-knows-how-long. The standing committee on Justice simply must take up the issue when it meets on Wednesday. If it doesn’t, if the Liberal MPs on the committee obstruct an investigation, that will only reinforce the impression that they are under the thumb of the PMO.

We are so far from Mr. Trudeau’s promise to reverse decades of ever-greater concentration of power in the Prime Minister’s Office. “Actually, it can be traced as far back as my father, who kicked it off in the first place,” Mr. Trudeau told the CBC’s Peter Mansbridge during the election campaign. “I actually quite like the symmetry of me being the one who ends that.”

“As you can imagine, I took a strong interest in that commitment,” said Donald Savoie, a political scientist at University of Moncton who has written extensively on the concentration of power within government. “If anything he has strengthened governing from the Centre,” he said in an e-mail exchange.

From the start, Mr. Trudeau’s advisers, especially his principal secretary and close personal friend, Gerald Butts, exercised tight control over a cabinet filled with rookies, including Ms. Wilson-Raybould. Few ministers were willing to stand up to the directives that routinely came their way from the PMO.

But Ms. Wilson-Raybould earned a reputation for pushing back. She is strong-willed, accustomed to getting her way and impossible to bully. Her unwillingness to defer in the SNC-Lavalin affair may have led to her demotion from Justice to Veterans Affairs and ultimately to her resignation.

A defiant Justin Trudeau told reporters on Tuesday night he was “surprised and disappointed” by the minister’s resignation. Neither he nor his government have done anything wrong, he said, in its treatment of SNC-Lavalin or anyone else. “Our government did our job properly, and according to all the rules.”

Perhaps that approach will work. But Mr. Trudeau must know that Ms. Wilson-Raybould’s version of events will come out. And he must know how much damage has been done.

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