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OTTAWA -- A lawyer for Maj.-Gen. Dany Fortin painted the senior military officer's abrupt removal as head of Canada's COVID-19 vaccine rollout in May as a threat to the independence of the Canadian Armed Forces.

The comments came Tuesday during the first day of a two-day hearing in which Fortin's legal team led by Thomas Conway asked a Federal Court judge to reinstate their client to his former job at the Public Health Agency of Canada, or a similar position.

Fortin's lawyers have previously alleged the decision to remove the Afghan war veteran was unreasonable, lacked procedural fairness and involved inappropriate political interference by the Liberal government in the military's internal affairs.

Conway repeatedly hit upon that last point, arguing that because Fortin was still a serving military member, only acting defence chief Gen. Wayne Eyre had the power under the National Defence Act to remove him from the vaccine campaign.

In that vein, Conway questioned why the government did not provide an affidavit from Eyre or other evidence to prove Canada's top military officer was ultimately responsible for removing Fortin from his position on May 14, rather than Eyre's political masters.

Those masters include Prime Minister Justin Trudeau, Defence Minister Harjit Sajjan, Health Minister Patty Hajdu and Janice Charette, clerk of the Privy Council.

"That's all that was required to clear up this controversy," Conway told Justice Ann Marie McDonald, later adding: "The silence of the acting chief of defence staff speaks volumes."

Court was also shown a clip of an interview Hajdu did with CTV on May 30 in which she said she "agreed with the (PHAC) president (Iain Stewart) that Maj.-Gen. Dany Fortin should be relieved of his duties with the Public Health Agency."

Conway pointed to those comments, handwritten notes from Eyre and what he described as a lack of transparency from the government as proof Fortin's removal was both politically motivated and a threat to military independence.

"This application exposes a serious breach of that proper ordering of civilian control that Parliament contemplated in the National Defence Act by political actors outside the chain of command," he said.

"It is an insidious breach that, if left unchecked, will have serious and negative repercussions for it will signal that a new norm is in place. One that permits political actors to seed the chain of command with members who are not committed to the chain of command."

Conway's colleague, Natalia Rodriguez, later argued that there was also no reason to believe that keeping Fortin in his position at PHAC represented a risk to others.

Fortin was removed from his position five days before military police referred a case of sexual misconduct to the Quebec prosecution office. The senior officer was charged last month with one count of sexual assault dating back to 1988.

He has denied any wrongdoing and his criminal defence is being led by a different legal team.

Conway on Tuesday was facing off against Justice Department lawyer Elizabeth Richards, who at one point appeared to accept that others beyond Eyre were involved in the decision to remove Fortin.

"(Fortin) alleges that the minister of health, the minister of national defence, the Privy Council Office and the prime minister made that decision," she said. "You'll hear tomorrow that there's no dispute about the involvement of those individuals."

Richards was scheduled to respond to Conway's arguments in earnest on Wednesday.

Yet she suggested during her own motion earlier in the day asking McDonald to toss Fortin's case that if the senior military officer was unhappy with his removal from the vaccine campaign, he should have filed a grievance with the military.

"The military grievance process is established exactly for that reason: to deal with any manner of complaints, any issue whatsoever, about the administration of the Canadian Armed Forces," Richards told the court.

"The applicant hasn't even tried, hasn't even filed a grievance," she later added.

Conway in turn argued the grievance process was not the appropriate venue given allegations the decision to remove his client was made by the Liberal government and not Eyre.

"The decision was made outside of the chain of command of the Canadian Armed Forces," Conway said of Fortin's removal. "The Canadian Armed Forces has no authority to review decisions of ministers of the Crown."

Conway also noted concerns raised about the military grievance system and its failure to deal with complaints in a timely manner, including by retired Supreme Court justice Morris Fish in his recent review of the military justice system.

Richards shot back that such complaints were purely speculative, and that if McDonald allowed Fortin's case to go forward, it would open the door to other Canadian military members also sidestepping the grievance process by taking their complaints to court.

This report by The Canadian Press was first published Sept. 28, 2021.