Gen. Tom Lawson, Canada's chief of defence staff, describes the allegations in the latest edition of Maclean's magazine as "disturbing."
Lawson says sexual misconduct is not tolerated within the military, a message he intends to reinforce throughout the chain of command.
The magazine, which hit newsstands today, contains a series of interviews with alleged victims, and uses access-to-information records to track military police investigations over a decade.
Lawson did not acknowledge specific cases, but says the military will pursue all allegations of sexual misconduct while protecting complainants from reprisals.
In a statement from Mexico City, where he's meeting with his U.S. and Mexican counterparts, Defence Minister Rob Nicholson says he's ordered Lawson to get to the bottom of the matter.
The issue has the potential to tarnish the credentials of the Conservative government and Nicholson, a former justice minister. Both have long championed tough-on-crime legislation and the rights of victims of crime.
Nicholson says he was "deeply angered" to read of the allegations.
The Maclean's article comes just weeks after a pair of high-profile cases made headlines across Canada.
The former commanding officer of the army's main training base in western Canada was found guilty of sexual assault in early April.
A military judge found that Maj. David Yurczyszyn, who was once in charge of CFB Wainwright in Alberta, groped a woman's breast at a reception following Remembrance Day services in 2012.
At the beginning of his court martial, Yurczyszyn pleaded guilty to a charge of drunkenness under the National Defence Act, but he denied intentionally grabbing the woman.
Police in eastern Ontario also recently issued a public appeal for victims to come forward following the arrest of a soldier at Garrison Petawawa, Ont.
Cpl. Derrick Gallagher, 31, was taken into custody on March 31, and initially charged with eight counts of sexual assault and two counts of voyeurism contrary to the Criminal Code.
Police later added 18 additional charges.
Investigators said they know of 18 alleged victims and are still trying to identify as many as 50 women who may have been victimized without their knowledge.
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