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National Defence waited nearly two months to remove Major-General Dany Fortin from his military duties and as head of Canada’s vaccination rollout because it was scrambling to deal with a series of allegations of sexual misconduct involving at least seven high-ranking officers, sources say.

The federal government replaced Maj.-Gen. Fortin on Monday, naming Brigadier-General Krista Brodie as head of Canada’s vaccination campaign effective immediately. The Public Health Agency of Canada said she has played a key role in the vaccine rollout as part of a deployment to the agency in November.

Maj-Gen. Fortin was informed Friday that he had to step aside but his lawyer said he was never told the nature of a three-decade-old allegation of sexual misconduct until two days later when he was contacted by a CTV reporter.

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“It is a news reporter who informed Major-General Fortin of the allegation against him Sunday, May 16. This took him completely by surprise. He vigorously and categorically denies this allegation,” Commander Mark Letourneau said in a statement to The Globe and Mail on Monday.

The reporter told Maj-Gen. Fortin that a female complainant had gone to military police in March, alleging that he exposed himself while a student in 1989 at the Royal Military College in Saint-Jean, Que.

Two sources confirmed the allegation was made in March, but said the delay in asking Maj-Gen. Fortin to leave his post was because National Defence was dealing with at least seven complaints against senior officers. The department wanted to make sure that proper processes were followed to avoid possible lawsuits, they said. The Globe and Mail is not revealing the sources because they were not authorized to publicly discuss the matter.

The Canadian Armed Forces have been rocked by a sexual-misconduct crisis that has blemished the military, forced a number of major commanders to step aside and resulted in the appointment of former Supreme Court justice Louise Arbour to study the creation of an independent watchdog to investigate complaints of sexual harassment, sexual assault and rape.

Three military police investigations are known to be under way into the conduct of former chief of the defence staff Jonathan Vance, Admiral Art McDonald, who succeeded Mr. Vance, and Vice-Admiral Haydn Edmundson. 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 sources noted that Adm. McDonald was asked to voluntarily leave his post in February several weeks after a complaint of sexual misconduct was made against him to military police.

Brig.-Gen. Brodie, the new head of the COVID-19 vaccine rollout, joined the Canadian Armed Forces in 1989. During her time in the army, she has commanded platoons, a company and a battalion. She has been deployed to Croatia, Bosnia and Afghanistan. Brig.-Gen. Brodie also served with both NATO and the United Nations. She is married with three children.

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While there is some sympathy at National Defence headquarters for Maj-Gen. Fortin’s situation, the sources said Acting Chief of Defence Staff Lieutenant-General Wayne Eyre and deputy minister Jody Thomas took the complaint seriously. They have decided that all complaints – no matter how long ago – must be dealt with through a proper military investigation, sources said.

The Prime Minister’s Office declined to say when it was informed of the allegation against Maj-Gen. Fortin, who has won the government’s approval for managing the distribution of vaccines to combat the COVID-19 pandemic.

“These matters are handled by authorities and CAF officials. When appropriate, the PMO is provided status updates on senior personnel decisions by the Privy Council Office,” press secretary Alex Wellstead said in an e-mail.

NDP defence critic Randall Garrison said the Liberal government should have acted on recommendations contained within a 2015 report from former Supreme Court justice Marie Deschamps that detailed a highly sexualized culture in the Forces that is hostile to women and LGBTQ members.

“Service people and all Canadians are watching this unfold and wondering just what is going on and how years of inaction from the government has brought us to this point,” Mr. Garrison said.

The Trudeau government has been under political pressure in recent weeks since former military ombudsman Gary Walbourne told a parliamentary committee that he presented Defence Minister Harjit Sajjan with an allegation about Mr. Vance in March, 2018, when he was chief of the defence staff. Mr. Sajjan declined to see the evidence.

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Although the Prime Minister’s Office was immediately informed of the allegation, no further action was taken after Mr. Walbourne emphasized that the complainant had come to him in confidence.

Employment Minister Carla Qualtrough said Monday that the country’s vaccine effort will not be affected by Maj-Gen. Fortin’s departure from his role.

Canada has had 20 million doses delivered to provinces as of last Friday, she added, saying another 50 million are on the way before the end of June.

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