Canada's military justice system was rocked Thursday after military police took the unprecedented step of charging the Forces' highest-ranking judge.

Col. Mario Dutil has been accused of one count of committing an act of a fraudulent nature, one count of wilfully making a false entry in an official document, and one count of conduct to the prejudice of good order and discipline.

The charges relate to allegations that Dutil engaged in an inappropriate personal relationship with a subordinate, and that he knowingly signed a travel claim containing false information, according to a military spokesman.

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While none of the charges have been proven in court, the very fact that they were laid had officials throughout the Department of National Defence scrambling to understand the potential impacts – and how the case would proceed.

Military police first started investigating Dutil in November 2015 after receiving a complaint that he had engaged in an inappropriate relationship with a subordinate, according to spokesman Maj. Jean-Marc Mercier.

The alleged relationship is believed to have lasted from November 2014 to October 2015 and while consensual, was not permitted under military regulations, Mercier said.

It was during the course of their investigation into that relationship, Mercier said, that military police uncovered evidence to suggest Dutil knowingly signed a travel claim containing false information in September 2015.

It's believed Dutil is the first person to be charged while serving as the chief military judge, and the case will now proceed through the military justice system in which he serves as a prominent member.

Judge Advocate General Commodore Genevieve Bernatchez took the unusual step of issuing a statement in which she acknowledged that the charges present "unique challenges for the Canadian military justice system."

However, she said the charges are a reminder that no one is above the law and added that she's "fully confident that we have the processes in place to deal with the current circumstances fairly and in accordance with the law."

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Senior military officials briefing reporters on background Thursday said only the federal cabinet can appoint or remove a chief military judge, meaning Dutil will remain in his position for the foreseeable future.

However, they said he was not scheduled to hear any cases.

Exactly how Dutil's case will be handled is also unclear at the moment, including whether one of the three other military judges over which he presided will end up hearing the case against him.

There is a possibility that a special prosecutor could be asked to handle the case, the senior officials said.

This isn't the first time that Dutil, who took over his current role in 2006, has been accused of violating the military's rules on personal relationships.

But a special committee of three judges dismissed a complaint in April 2016 on the basis that it did not have any impact on Dutil's conduct as a judge. Military police did not lay any charges at that time.

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Officials would not say whether the complaints related to the same alleged relationship.

A conviction for committing an act of a fraudulent nature carries a maximum penalty of two years less a day in prison while wilfully making a false entry in an official document carries a penalty of three years less a day.

The maximum penalty for prejudicing good order and discipline is dismissal from the military with disgrace.