Investigators have seized the cellphone allegedly used and sent it to the technical crime unit of the Canadian Forces National Investigation Service in Ottawa for analysis.
At the time of the incident the Montréal was near Mayport, Fla., at the tail end of a two-and-a-half month deployment taking part in three military exercises.
The woman swore and yelled at the man, documents say.
Court documents obtained by CBC News say the female sailor reported that on Nov. 15 she was in her bunk playing solitaire when an arm and a dark cellphone appeared over the curtain that offers privacy. The lights were off, aside from red ambient lighting.
The woman swore and yelled at the man, the documents say, and he crept out. Men are not allowed in the women's area unless following specific orders and only if they sign a log book and announce themselves.
While the sailor did not know his name, she identified him the next day during meal time in the mess, according to court documents. When confronted by superiors, the male sailor initially refused to hand over the cellphone, and only did so after his locker was searched, according to an affidavit sworn by a military investigator to obtain a search warrant for the phone.
Stamping out 'abhorrent behaviour'
Rear Admiral John Newton, commander of Maritime Forces Atlantic, says the military is moving swiftly to determine if this was a criminal act or if administrative sanctions are warranted.
He says the accused was flown off the ship to the U.S., and then on to Canada so he and the alleged victim would be separated.
Newton said the immediate separation is part of protocols developed to stamp out "abhorrent behaviours" in the military, which has come under criticism for how it has handled past cases of sexual misconduct.
"These sort of very mechanistic steps are now moving with more rigour and vigour," he said in an interview. "There's no doubt in the leadership's mind that we're taking this action, and there's no doubt, I think, in our subordinates' minds that we've created this space for them to report allegations."
Newton said following deployment the alleged victim returned to her home unit in another part of Canada. The accused is back on duty, he said, and the military is awaiting the results of the cellphone analysis before deciding what to do next.
Military police could charge the man and he would answer the charges in a court martial or in the regular court system.
Following the incident, the Montréal's executive officer, Lt.-Cmdr. Nancy Setchell, convened a meeting of the roughly two dozen women on board.
Newton says she asked if there was an undercurrent of voyeurism on the ship. The women told her they consider the problem to be restricted to one individual.
The investigation comes as military police are also looking into an allegation of sexual assault in November on board another Canadian ship, HMCS Athabaskan.
HMCS Athabaskan. (Photo: Master Corporal Charles Barber, staff photographer)
Both allegations come months after a scathing report by a former Supreme Court justice that called sexual misconduct in the military "endemic."
But one retired colonel who has criticized how the military has handled cases of sexual misconduct is praising the professionalism of the HMCS Montréal investigation and how the chain of command has dealt with the situation.
"If every investigation and every complaint is handled in this way, then the Department of National Defence, more particularly Canadian Forces, will be able to turn the page," says Ottawa lawyer Michel Drapeau, who has reviewed the affidavit used to obtain a court order to seize and analyze the phone.
"Most important in all of that, to gain the trust and confidence of would-be victims that they have sufficient confidence [in] the chain of command and military justice system that when victimized they can come forward and report the alleged crime."