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Maj.-Gen. Dany Fortin, Vice-President of Logistics and Operations at the Public Health Agency of Canada, speaks during a technical briefing on the roll-out of COVID-19 vaccines, in Ottawa, on Dec. 3, 2020.

Justin Tang/The Canadian Press

The Canadian Forces commander in charge of Canada’s vaccine logistics has stepped aside and is facing a military investigation for alleged sexual misconduct, according to a source.

The Department of National Defence announced late Friday that Major-General Dany Fortin has left his post while he faces an investigation by military police. The department provided no further details.

“Major-General Dany Fortin has left his assignment with the Public Health Agency of Canada, pending the results of a military investigation,” the department said in a statement. “Acting Chief of the Defence Staff, Lieutenant-General Wayne Eyre, will be reviewing next steps with Major-General Fortin.”

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A source told The Globe and Mail that military investigators are looking into an allegation of sexual misconduct that took place before Maj.-Gen. Fortin became a general in 2015. The source said that the female complainant has requested that the allegation not be shared publicly. The Globe is not identifying the source because they are not allowed to discuss the matter.

Maj.-Gen. Fortin was a rising star in the Armed Forces and was chosen in November, 2020 to handle logistics and operations for the Public Health Agency of Canada to help in the procurement and distribution of vaccines to combat the COVID-19 pandemic.

The source said Lt.-Gen. Eyre and Jody Thomas, deputy minister of National Defence, have decided that all credible complaints – no matter how long ago – must be dealt with through a proper military investigation.

The source said Gen. Eyre has also requested a thorough review of all generals and naval commanders in the Armed Forces to determine if they may have issues of misconduct that could surface.

The Armed Forces has been shaken by a sexual-misconduct crisis that has tarnished the institution and forced a number of major commanders to step aside, including chief of the defence staff Admiral Art McDonald, who voluntarily left his post in February. He is under investigation for an unspecified allegation of sexual misconduct.

The investigation into Adm. McDonald came in the wake of the controversy surrounding the former defence chief Jonathan Vance, who retired.

Mr. Vance is also under investigation by the Canadian Forces National Investigation Service after allegations – first reported by Global News – that he had an inappropriate relationship with a female subordinate. Global News also reported that he sent an e-mail to a female subordinate in 2012. He reportedly suggested the two of them could go to a clothing-optional resort.

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Mr. Vance denied any wrongdoing in an interview with Global News earlier this year, but otherwise has not commented.

Vice-Admiral Hayden Edmundson also stepped aside earlier this year after allegations of sexual assault and misconduct, while Major-General Peter Dawe, commander of special forces, left his post after it was revealed that he wrote a letter of support for a soldier convicted of sexual assault of a female member.

The controversy has sparked a national conversation on sexual misconduct in the Canadian Armed Forces, with female soldiers coming forward with complaints ranging from verbal harassment to sexual assault and rape.

It led to hearings by the House of Commons National Defence committee and the Status of Women committee.

In testimony before the defence committee, former military ombudsman Gary Walbourne said he raised an allegation of sexual harassment against Mr. Vance with Defence Minister Harjit Sajjan in 2018.

Mr. Sajjan informed his chief of staff, who alerted Elder Marques, a former senior adviser to Prime Minister Justin Trudeau. The senior adviser then told Mr. Trudeau’s chief of staff, Katie Telford, and they agreed to refer the matter to then-Privy Council clerk Michael Wernick, who asked an official in his office to investigate.

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No further action was taken after Mr. Walbourne emphasized that the complainant had come to him in confidence.

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