Quebec prosecutor's office to decide on possible charges against Maj.-Gen. Dany Fortin

A branch of the military police investigating an allegation of sexual misconduct involving Maj.-Gen. Dany Fortin has now referred the matter to a Crown official to decide whether criminal charges should be laid.

The Department of National Defence (DND) issued a terse three-line statement late Friday saying Fortin was leaving his post leading Canada's vaccine logistics at the Public Health Agency of Canada and his future would be decided by the acting chief of the defence staff.

In a statement today, the Canadian Forces Provost Marshal said the Canadian Forces National Investigation Service (CFNIS) has sent the file to the Quebec's director of criminal and penal prosecutions, "who is the charge laying authority for criminal and penal prosecutions in the province."

A senior government official speaking on background said the referral to the prosecutor's office is what prompted Fortin's sudden departure from his role on Friday.

CBC News has confirmed the investigation involves an allegation of sexual misconduct that predates 2015 and the military's now-defunct Operation Honour campaign, which was intended to stamp out inappropriate behaviour in the military.

Three separate confidential sources, who were not authorized to speak publicly because of the sensitivity of the file, described it as an older claim but declined to be more specific. The Globe and Mail was the first to report the allegation against Fortin was sexual in nature.

Police may be seeking 'legal advice' from prosecutor

Rory Fowler, a retired military legal officer now in private practice, said that military police investigators may be trying to determine if they have sufficient evidence to support a charge. He also said there could be a jurisdictional issue, depending on how far back the allegation dates.

"Military police are accustomed to getting legal advice from the prosecutor before laying a charge," said Fowler. "Seeking pre-charge legal advice doesn't mean charges would be laid."

Michel Drapeau, a retired colonel who practises military law, said that if the alleged incident happened before 1998 and the military considers it a sexual assault allegation, military authorities would not have jurisdiction.

Prior to 1998, the civilian justice system handled sexual assault cases involving military members.

Fortin's lawyer, Cdr. Marc Létourneau, has said his client knew about the investigation some time before Friday but only learned the specifics of the allegation on the weekend. He said Fortin will fight the allegation.

"It is a news reporter who informed Major-General Fortin of the allegation against him Sunday, May 16," Letourneau said in a written statement.

"This took him completely by surprise. He vigorously and categorically denies this allegation."

Prime Minister Justin Trudeau acknowledged on Tuesday that he learned about the investigation several weeks ago. Defence Minister Harjit Sajjan found out around the same time as the prime minister, his office said. 

A senior government official, speaking on background, told CBC News the acting top military commander, Lt.-Gen. Wayne Eyre, was first briefed on the investigation into Fortin in mid-March but was not told specifics.

After weighing the risks, Eyre made a command decision to keep Fortin in his role, said the confidential source, who was not authorized to speak publicly because of the sensitivity of the file.

Senior officials in the Prime Minister's Office were told of the investigation and that Fortin was staying in his role for the time being, said the source.

CBC News asked Sajjan's office today whether he knew in March if the allegation was sexual in nature. Sajjan's office didn't answer that question.

"This inquiry deals with the potential substance of an allegation and, as an independent investigation process is underway, it would be inappropriate to comment further at this time," said Sajjan's press secretary Daniel Minden in a statement to CBC News.