Global News can confirm that the investigation is linked to a sexual misconduct allegation dating from before Fortin was a general.
The Department of National Defence announced Fortin’s departure in a statement Friday.
“Today, Major-General Dany Fortin has left his assignment with the Public Health Agency of Canada, pending the results of a military investigation,” a spokesperson said.
“Acting Chief of the Defence Staff, Lieutenant-General Eyre will be reviewing next steps with Major-General Fortin. We will have no further comment.”
Global News has confirmed the investigation is being conducted by the Canadian Forces National Investigation Unit, the specialized unit of military police that handles “serious and sensitive matters.”
Defence Minister Harjit Sajjan also issued a statement following the announcement of the probe.
“As I have stated previously, I am committed to working to build a true culture of inclusion for the Canadian Armed Forces and the Department of National Defence, where everyone is treated with dignity and respect. We are committed to this lasting change – one that sheds toxic and outdated values, practices, and policies,” he said.
“The Acting Chief of Defence Staff has advised me that MGen Fortin has stepped aside. As there is an ongoing investigation, I will have no further comment at this time.”
Sajjan added the government remains focused on the vaccine rollout.
Details of the sexual misconduct allegation that sparked the investigation were first reported by the Globe and Mail Friday.
The Canadian military is grappling with what experts call an institutional crisis amid investigations into allegations of sexual misconduct made against multiple current and former senior leaders.
A spokesperson for the Department of National Defence said no details are being released because the investigation is ongoing.
Fortin was named as vice president of logistics and operations at the Public Health Agency of Canada in November 2020 and tasked with overseeing logistical planning for the vaccine rollout.
He also runs the National Operations Centre.
Prior to taking on the role, he was chief of staff at the Canadian Joint Operations Command and from November 2018 to the fall of 2019, he held command of the NATO mission in Iraq.
It is unclear who will replace him as military head of the vaccine rollout.
The Public Health Agency of Canada would not comment on what Fortin’s departure means for the rollout. The agency referred all questions to the Department of Defence.
In an email Saturday, Health Canada told Global News that questions about the next steps for Canada’s vaccine rollout plan, including who will replace Fortin, will be answered on Monday.
–With files from Global’s Mercedes Stephenson, Sean Boynton and Hannah Jac