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He has alleged investigators inadequately documented interactions with the complainant in his case, failed to ask crucial questions and interview key witnesses, and improperly handled evidence.

Whelan was head of the military's personnel in 2021 when a woman who had been his subordinate accused him of having an inappropriate sexual relationship with her. 

He was put on leave during the investigation, and the allegation became the subject of a news story in October 2021. 

Whelan was charged by military police in 2022 with two counts of conduct to the prejudice of good order and discipline. 

He pleaded not guilty. Military prosecutors took the case to a court martial the next year, but they dropped the charge related to alleged sexual misconduct on the first day of hearings. 

The second charge was dropped days later, after the judge ruled that certain evidence was not admissible. 

In his complaint to the Military Police Complaints Commission, Whelan said he believes the charges against him were coerced, and that some of the shortcomings in the investigation were because of improper influence from the chain of command "and a desire for a specific outcome."

He also alleges that leaks to the media about the allegations against him were not properly investigated and suggested this may indicate the military police were complicit in enabling those leaks. 

The head of the commission says Whelan's allegations against the military police are significant. 

"If substantiated, they could amount to a deliberate failure to properly investigate the serious allegation of sexual misconduct, possibly because the investigation was conducted with the objective of reaching a predetermined outcome," said the commission's chair, Tammy Tremblay. 

A news release announcing Tremblay's decision to investigate the case said while the seriousness of the issues in this complaint "could warrant public hearings," she has decided it would be more expeditious to investigate without a hearing at this time. 

Tremblay noted that while Whelan asked for a broad, systemic investigation into sexual misconduct cases involving senior military officers, her office does not have a mandate to do an investigation of that type. It does, however, have the ability to consider and address systemic issues in individual complaints.

"Sexual misconduct in the military is an important issue that demands rigorous investigations," Tremblay said in her decision. "However, it would be problematic if, in investigating allegations of sexual misconduct, the military police were to become, consciously or unconsciously, tainted by biases against victims or suspects."

Tremblay's final report will be made public.

Whelan filed a lawsuit in May against the federal government and his accuser. 

The statement of claim says the military and Defence Department should publicly apologize for the "abuse of office, negligent investigation, malicious prosecution and involvement in the media leaks that destroyed his reputation and career."

It accuses the defendants of conspiring to minimize the political fallout of the allegations.

Throughout 2021, the Armed Forces was embroiled in controversy after several high-ranking leaders were publicly accused of sexual misconduct. Some were criminally charged.

The government launched an external review, headed by former Supreme Court justice Louise Arbour, who recommended sweeping changes to the military's culture and the way it deals with sexual misconduct cases.

Another of the high-profile cases in 2021 also led to a lawsuit against the federal government. 

Maj.-Gen. Dany Fortin was removed as head of Canada's COVID-19 vaccine rollout campaign in May 2021 while he was under investigation for an allegation dating from 1988.

He was charged with one count of sexual assault in August 2021 and was later acquitted after a trial in the civilian Quebec Superior Court. The Armed Forces also cleared him of wrongdoing.

Fortin filed a lawsuit in March 2023 against 16 high-ranking officials, including Prime Minister Justin Trudeau, Eyre and the Liberal cabinet ministers who held the defence and health portfolios at the time of the accusation.

He reached an undisclosed settlement with the government in October 2023.

This report by ºÃÉ«tvwas first published Dec. 11, 2024.