OTTAWA -- The president of the Public Health Agency of Canada (PHAC) Iain Stewart says that he was first informed of a potential “issue” regarding the military general leading Canada’s vaccine rollout in March, but he wasn’t aware of the nature of it until the day before Maj.-Gen. Dany Fortin left his post.

Speaking at the House of Commons Health Committee on Friday, Stewart said that he was informed in the third week of March by the deputy minister at the Department of National Defence that: “There was an issue affecting Maj.-Gen. Fortin, but the nature was not apparent.”

“And that was just kind of a heads up that there was a potential issue,” he said. Fortin had been seconded to PHAC to lead the logistical side of the COVID-19 vaccination effort. 

As CTV News has exclusively reported, according to sources, military police received a formal complaint against Fortin in March, alleging a “historical sexual assault.” The incident, sources say, allegedly dates back 32 years to early 1989 when Fortin was a student at the Royal Military College in Saint-Jean, Que.

Defence Minister Harjit Sajjan was aware in March that the military investigation was underway, and Prime Minister Justin Trudeau said Tuesday that he was also made aware of the investigation “a number of weeks ago,” but he did not receive details about what was alleged.

It was then on May 13—one day before the Department of National Defence announced in a brief statement that Fortin would be stepping away from his role “pending the results of a military investigation”— that Stewart said he was informed of “a specific allegation moving into a process.”

Stewart told MPs that he did discuss the allegation with Health Minister Patty Hajdu in the afternoon on May 13, and that was the day it was decided that “there needed to be a change.”

That Thursday afternoon was also the day when Fortin participated in his last vaccine rollout technical briefing, appearing as the face of the logistical component of federal government’s mass vaccination effort.

According to Fortin’s lawyer, while Fortin had known a few weeks prior to his departure on May 14 that a military investigation had been initiated, Fortin was not aware of the specific allegation until CTV News contacted him on the weekend following.

Stewart said that between March and May he did not involve himself in the matter other than speaking about it with his chief of staff, nor did he ask for more information because to him, it was a Canadian Armed Forces matter. Though Stewart said he did start thinking about what would happen if he needed to find a new vaccine lead.

“At that stage the potential issue was not clear what it was, and nor is it clear what the repercussions were going to be,” Stewart said.

The military investigation into the allegation of sexual misconduct against Fortin has now been handed over to Quebec’s civilian prosecution service. As the charge-laying authority for criminal and penal prosecutions in the province, it will be up to that office to determine whether and how to proceed.

Fortin, through his lawyer, has said he “completely denies” any wrongdoing. The allegation has not been tested or proven in court.

Brig.-Gen. Krista Brodie has been named as the new logistical lead on the COVID-19 vaccine rollout.

During her debut vaccine technical briefing on Thursday, Brodie said that the job of receiving and distributing millions of COVID-19 vaccine doses a week is “on track,” despite the shakeup at the helm, and ongoing uncertainty around shipments from three of the four authorized vaccine manufacturers.

“We are focused on the goal, and we'll keep working tirelessly to provide vaccines to Canadians,” she said.

On Friday, Stewart also offered new projections on when Canada may hit key markers in the push to fully vaccinating everyone who wants to be by the end of September.

He said that PHAC anticipates 20 per cent of Canadians to be fully vaccinated by “late June,” and that by “the back end of July, or August” 50 per cent of the population should have received their second dose.

With files from CTV News’ Annie Bergeron-Oliver and Kevin Gallagher.