Photo: The Canadian Press

Justin Trudeau says he first learned weeks ago that the general overseeing Canada's vaccination campaign was under investigation, which the prime minister described on Tuesday as "not an ideal situation."

The comments during a regular COVID-19 update represented the first from Trudeau since the Department of National Defence announced late Friday that Maj.-Gen. Dany Fortin was being replaced because of an unspecified military investigation.

A source who was granted anonymity because they were not authorized to discuss the matter publicly told The Canadian Press that the investigation relates to an allegation of sexual misconduct.

CTV News has reported that Fortin is being investigated for having allegedly exposed himself to a woman while he was an officer cadet at the Royal Military College in Saint-Jean, Que., in 1989.

Fortin's military lawyer Cmdr. Mark Letourneau says his client only learned of the details of the allegation when reached by a reporter on Sunday, and that he categorically denies any wrongdoing.

Trudeau told reporters that he was not given the details of the allegation against Fortin as he was pressed on why the Liberal government did not replace the general immediately after it learned of the investigation.

The prime minister also deferred to military authorities when asked why more information about the nature of the investigation has not been publicly disclosed by the government or Department of National Defence.

Some experts as well as Conservative Leader Erin O’Toole have criticized the secrecy surrounding Fortin’s removal on Friday, which was announced in a terse three-line statement from the Defence Department.

"I understand all these questions, and they're very legitimate questions," Trudeau said.

"This is also not an ideal situation to be in, particularly in this moment of crisis, in this moment of importance, on the vaccine rollout. But it is really, really important that we have proper processes in place and that any concerns be followed up on."

The Liberal government and military have both been under fire over their handling of several other cases involving allegations of misconduct against senior officers, including former chief of the defence staff general Jonathan Vance.

The House of Commons' defence committee has been specifically drilling into why the government didn't do more after then-military ombudsman Gary Walbourne flagged an allegation against Vance to Defence Minister Harjit Sajjan in March 2018.

Committee members were scheduled to meet on Tuesday afternoon to discuss next steps after months of testimony from various witnesses, including Walbourne, Sajjan and senior members of Trudeau’s office.

For his part, Trudeau sought to reassure Canadians that the vaccination campaign, which is now being overseen by Brig.-Gen. Krista Brodie, will not be negatively affected by Fortin's departure.

The Public Health Agency of Canada announced late Monday that Brodie, a 30-year veteran of the military who was working with Fortin on the vaccination campaign, would be taking over.

"Brig.-Gen. Brody had already played a key role in the vaccine rollout with the Public Health Agency," Trudeau said. "She, along with the team that's been there since day one, is ready and able to get millions of doses to Canadians in the coming weeks."