Gen. Tom Lawson, Canada's chief of defense staff, described the allegations in the latest edition of Maclean's magazine as "disturbing."
The year-long investigation, conducted by Maclean's and its French-language sister publication L'Actualite, also suggests that some assaults may have been covered up.
The report in Maclean's published this week contains interviews with alleged victims, and uses access-to-information records to track military police investigations over a decade.
The reporters also attended court martial proceedings. The victims in the report included a woman in her 50s who allegedly endured 30 years of abuse during her time in the military and a woman in her 40s who was allegedly raped in Afghanistan.
According to statistics obtained through Canada's Access to Information Act, five individuals in the Canadian military community become victims of sexual assault every day. The numbers show military police have received between 134 and 201 complaints of sexual assaults every year since 2000, which averages out to 178 per year.
Victims say their cases are ignored and that going public jeopardizes their career.
"I do not accept from any quarter that this is merely a part of military culture; it is not," Lawson said in response to the report. "Sexual misconduct of any kind is not and will not be tolerated within the CAF (Canadian Armed Forces), and this is a message that I reinforce throughout the chain of command."
Lawson did not acknowledge specific cases, but says the military will pursue all allegations of sexual misconduct while protecting complainants from reprisals.
Defense Minister Rob Nicholson also issued a statement after the report was published saying that he was "deeply angered to learn of the sexual assault allegations in the military." He said he's ordered Lawson to get to the bottom of the matter.
"Since 2006, our government has continuously fought on behalf of victims and enhanced the laws in this country to combat sexual assault," said Nicholson.