Maj. David Yurczyszyn was removed Thursday from the top post at CFB Wainwright, a sprawling training base 200 kilometres southeast of Edmonton.
In addition to the criminal accusation of sexual assault, he faces charges of drunkenness and disgraceful conduct under sections of the National Defence Act.
The alleged offences occurred last Remembrance Day. The military is refusing to release any other details.
Brig-Gen. Christian Juneau, Commander Land Force Western Area, reacted to the allegations in a news release.
"The actions of Maj. Yurczyszyn have caused me to lose confidence in this officer's ability to effectively exercise the functions of command," he said.
"We expect the highest standard of professionalism and conduct from our leaders, especially those entrusted with command authority."
Military spokeswoman Lt. (Navy) Jessica MacDonald said Yurczyszyn is not in custody. He has been reassigned to desk duties and will work from home while an administrative review of his file is completed.
She confirmed Yurczyszyn was previously charged in another matter.
In a case that garnered some media attention, Yurczyszyn was accused in 2001 of making homemade porn and showcasing it at military parties, but a judge dismissed the charges the following year, ruling there wasn't enough evidence to support a conviction.
The porn tape featured another soldier having sex with a civilian woman — a university student — in the bedroom of a married quarters apartment on CFB Kingston. The video was made without the woman's permission.
Court heard so-called "porn and chicken" nights were a long-time ritual to help cadets unwind. They would often rent hotel rooms and watch sex videos while eating chicken.
The military began investigating after a female cadet complained to her squadron commander about the tape.
Yurczyszyn was charged under the National Defence Act with behaving in a disgraceful manner and with conduct to the prejudice of good order and discipline.
His lawyer argued he was simply in the wrong place at the wrong time and had little involvement in planning the video.
But in his decision, Judge Jim Prince said Yurczyszyn may not have been entirely blameless. "The accused was arguably more than a common bystander ... may even be said to have assisted."
Yurczyszyn could be heard in part of the tape that was played in court. He said "get her while she's drunk" and talked about where the camera should be placed in the bedroom.
Two other officers — the one who had sex with the woman and the other who lived in the apartment — were convicted on various charges and dismissed from the military.
At the time, Yurczyszyn was a second-lieutenant, a junior officer. He told the court he was relieved to have the charges dropped and just wanted to carry on with his job.
He next served in Petawawa and was stationed over the years at various other bases.
MacDonald said Yurczyszyn has completed three overseas tours — one in Bosnia and two in Afghanistan.
On his first trip to Afghanistan, he was part of a team that trained members of the Afghan military. On his second tour, he was part of a transition team that tied up loose ends before the Canadian Forces pulled out of the country.
He took over command of CFB Wainwright last June.
The base is used to train individual soldiers and military units in the field. It includes a high-tech manoeuvre training centre that allows commanders to simulate and plan battles, as well as mock-up villages that were used to train troops for service in Afghanistan.
The base, just outside the town of Wainwright, is considered the largest employer in the area. It has about 1,000 military and civilian employees.
This case against Yurczyszyn will now be reviewed to determine if there is enough evidence for a court martial. It's not known when that process will be finished.
Maj. Kevin Cadman of the Canadian Forces National Investigation Service, a unit within the independent Canadian Forces military police, said the case is being taken seriously.
"All members of the Canadian Armed Forces are expected to conduct themselves in an appropriate and professional manner at all times," he said.
"The Canadian Forces National Investigation Service and the military police consider these charges to be significant and have taken action accordingly."
Note to readers: This is a corrected story. A previous version wrongly suggested that Lt. Jessica MacDonald had confirmed details of previous charges.
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