Gen. Tom Lawson, the chief of defence staff, ordered the board of inquiry into the case of former master corporal Stephanie Raymond on Wednesday, one day after she was given a post-release promotion, a decoration and a certificate of service.
The commander of the army, Lt.-Gen. Marquis Haines, announced the inquiry in a statement, saying the technical investigation will look at how she was treated from the time she filed her initial harassment complaint until her release in December 2013.
The statement said "irregularities in administrative procedures" prompted the investigation, but the military did not explain what that means.
Raymond's case was featured on the covers of Maclean's and L'actualite magazines last year in articles that claimed sexual assaults had reached epidemic levels in the military.
She was described in the reports as a model soldier who suddenly became an "administrative burden" when she reported the alleged assault in 2011 to military authorities.
In response to the allegations in the report, Lawson convened an outside, independent report by a former Supreme Court of Canada justice, who is now in the process of assembling her findings.
The board of inquiry looks at military procedures and is not criminal in nature.
It does have the power to make recommendations for change.
"Every member of our army family needs to feel safe, supported and free to bring issues to the attention of the army leadership without fear of retaliation by his or her chain of command," Haines said in a statement.
"Mutual understanding, respect and trust are critical elements of our military ethos. It is the responsibility of army leadership to ensure those values are extended to all our men and women in uniform."