GATINEAU, QUE. -- A Quebec civilian judge has acquitted Maj.-Gen. Dany Fortin of sexual assault over an allegation that dates back to 1988.

Judge Richard Meredith said he believes the complainant was sexually assaulted, but said the Crown did not establish beyond a reasonable doubt that it was Fortin who had assaulted her.

Fortin was the military officer in charge of the federal government's COVID-19 vaccine rollout until May 2021, but he was removed from that position after the allegation came to light.

Shortly after the verdict Monday, he claimed to be the victim of political interference and told reporters he wants the military to restore him to an equivalent position.

The sexual assault allegation stemmed from Fortin's time at the military college in St-Jean-sur-Richelieu, Que., which the complainant also attended.

The complainant, whose identity is protected by a publication ban, testified in September that she woke up one night in her dorm room to find a man masturbating himself using one of her hands while his other hand was on her breast.

A Crown prosecutor told court the complainant waited until 2021 to bring the incident to light because she had retired and no longer feared career repercussions.

The complainant told the court that she is certain "without a doubt" that the perpetrator was Fortin.

But Fortin's lawyer cited inconsistencies between her testimony in court and her previous statements to investigators last year, including details of the incident.

A key point for the defence was that while the complainant said she told her then-boyfriend about the incident right afterward, he told the court he had no memory of such a conversation.

Meredith noted those inconsistencies Monday, as well as other contradicting testimony.

"The tribunal is otherwise convinced that the complainant was sexually assaulted. Generally, the complainant seemed sincere in this regard," Meredith said in French, as he read out his ruling to the court.

The judge said the lighting in the room was "very far from optimal conditions for seeing clearly" at the time of the alleged assault and noted that the complainant must have been in shock when the incident occurred.

"The reasons that explain why she had lived for so many years in silence, and which led her to ultimately file a complaint, are quite reasonable and credible," he said.

"The tribunal has no doubt of her sincerity. In this regard, the court sympathizes with her, considering the suffering she experienced. However, the tribunal's decision cannot be based on sympathy."

Meredith read out his decision over the course of 40 minutes in an exhaustive recounting of the evidence, testimony and relevant case law.

Upon hearing he had been acquitted, Fortin rubbed his hand over his face, his eyes watering. He later told reporters he was relieved by the decision.

"This is one important step in an ongoing process to prove my innocence and recover my reputation. I did not do what I was accused of," he said.

"Victims of assault need and deserve our support. But the fact, though, is that I was nowhere close to her room the night in question or at any other time."

Crown prosecutor Diane Legault said the verdict was a disappointment and she was not sure whether her team would seek to appeal.

"I think the judge decided to (give) the accused the benefit of the doubt," she said.

Fortin has accused Prime Minister Justin Trudeau and other senior members of the government of having turfed him for purely political reasons after the Liberals were accused of not doing enough to address sexual misconduct in the military.

He noted that the Federal Court of Appeal will rule on whether to hear his accusations in a separate, civil case.

A Federal Court judge tossed out his request for reinstatement in October, a decision Fortin is appealing, and his civil lawyer Natalia Rodriguez said Monday that both parties agreed to pause the matter pending the resolution of the criminal case. A panel hearing will likely take place this spring.

Fortin said he has effectively been on paid leave from the military, but claims he was never given anything in writing about being demoted from the vaccine task force.

"I was denied due process, and information about my case was mishandled and leaked," he said.

"The way this whole situation was allowed to unfold has irreparably harmed my career, my reputation and greatly impacted my family."

Defence Minister Anita Anand would not speak to Fortin's case. Her office said she had already spoken with media on other matters early Monday, and instead sent a written statement about work to weed out sexual misconduct in the Armed Forces.

The statement, attributed to Anand, noted that this includes a commitment to "select senior leaders whose conduct is beyond reproach."

In a statement with no attribution, the Canadian Armed Forces and the Department of National Defence said they will continue to offer the members involved "any support we can provide."

"We acknowledge the outcome of the criminal court proceeding and we will consider the implications of the judge's finding as it applies to our responsibilities and accountabilities going forward," the statement read.

Retired lieutenant-colonel Rory Fowler, who now practises as a lawyer, said the acquittal was "as convincing as you're ever going to get in a criminal trial," and this puts the military and government in a bind.

"The chief of the defence staff and his political masters are left in a circumstance where they've now got an officer whom a court has said is not guilty," he said.

"They have to justify why they're not going to allow them to return to work, or if they take further adverse action against him of an administrative nature."

This report by The Canadian Press was first published Dec. 5,2022.