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A senior military commander has been charged with two counts of breaching the Armed Forces’ disciplinary code, after a sexual-misconduct investigation by military police.

Lieutenant-General Steven Whelan was charged Wednesday with conduct prejudicial to good order and discipline under the National Defence Act, in connection with an inappropriate relationship with a subordinate, the military said in a statement.

The investigation “did not reveal any evidence to support the laying of charges under the Criminal Code,” the statement from the Office of the Canadian Forces Provost Marshal said.

The charges against Lt.-Gen. Whelan mark the end of the final, publicly disclosed, sexual-misconduct investigation that gripped the top brass and threw the Canadian Armed Forces into crisis last year. The investigations led to criminal charges against four current or retired commanders.

Prime Minister Justin Trudeau’s government has been criticized for failing to root out the problem and act on past recommendations.

Lt.-Gen. Whelan went on paid leave from his post as chief of military personnel in October, months after the investigation into his conduct was launched, and only after The Globe and Mail asked the military about the probe.

His lawyer, Phillip Millar, said Wednesday that Lt.-Gen. Whelan denies the allegations and will defend his case. Lt.-Gen. Whelan was charged under Section 129 of the National Defence Act, which Mr. Millar described as “not the most serious of offences.”

“It’s never good to be charged, but he’s charged with the lowest kind of charges out there,” he said, noting that they are not criminal and they relate to historical allegations. He said he looks forward to defending his client and said it’s “taken far too long to get to this point.”

The National Defence Act says individuals charged with breaching the code could face dismissal with disgrace or a lesser punishment.

In the Wednesday statement, the Forces said Lt.-Gen. Whelan’s case would stay in the military justice system, because the civilian system can’t try disciplinary-code cases. National defence spokesperson Daniel Le Bouthillier said he remains on paid leave.

The military has declined to disclose the number of senior commanders who are under investigation. Instead, the Forces confirm probes if information is leaked to journalists about a specific case and they request comment from the military.

Lt.-Gen. Whelan was put under investigation in the spring of last year, soon after he took over the military personnel post from another senior commander, who was put on leave, pending a separate investigation. As the chief of military personnel, Lt.-Gen. Whelan was responsible for rooting out bad behaviour in the Forces.

He replaced Vice-Admiral Haydn Edmundson, who went on leave in March, 2021. Vice-Adm. Edmundson was charged with sexual assault and committing indecent acts in December. He denies the allegations.

Vice-Adm. Edmundson was the third current or retired senior commander from the Canadian Armed Forces to face criminal charges in 2021.

Also charged was former chief of the defence staff Jonathan Vance. In March, Mr. Vance pleaded guilty to obstruction of justice and admitted that he tried to persuade a subordinate officer to lie to military police about their illicit affair.

Global News first reported allegations of sexual misconduct by Mr. Vance in February, 2021. At the time, two unnamed members of the Canadian Forces accused him of inappropriate behaviour. The military police investigation into the sexual-misconduct allegations ended with no charges directly related to the allegations.

Last year, Major-General Dany Fortin was charged with one count of sexual assault, which he denies. He is scheduled to face trial in September.

In June, military police charged retired lieutenant-general Trevor Cadieu with two counts of sexual assault. Mr. Cadieu was placed on leave after he was told he was the subject of a sexual-misconduct investigation last year. The Forces disclosed the investigation in October. At the time, Mr. Cadieu denied the allegations.

At the end of May, the federal government released a report from former Supreme Court justice Louise Arbour that found the military has failed to stamp out sexual misconduct. She said the Armed Forces should permanently move the prosecution of criminal-code sexual offences to the civilian system, turn over harassment complaints to the human-rights commission, and review the future of Canada’s military colleges.

To ensure her recommendations were implemented, Ms. Arbour said the government should “immediately” appoint an external monitor to track the progress of her report’s recommendations.

At the time, Defence Minister Anita Anand agreed to appoint a monitor as soon as possible. But almost two months later, no one has been given the post. On Wednesday, Ms. Anand’s spokesperson Daniel Minden said work is “well under way to finalize the process of establishing the position of the external monitor.” He provided no timeline for when someone would be appointed.

The government first received the recommendations from Ms. Arbour in March.

With a report from The Canadian Press

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