Lt. Derek de Jong left HMCS Preserver in September 2012 while it was docked in Key West, Fla., and was subsequently charged with being absent without leave.
Then a military prosecutor handling the case bumped the charge to desertion — one of the most serious charges in the military. A conviction carries the possibility of imprisonment, demotion, a $10,000 fine or dismissal from the military.
De Jong's court martial begins next week.
Maria de Jong, his wife, told CBC News she's going public with her husband's story because he can't.
"He can't speak. The military would not allow him to speak," she said Monday.
"It's against the rules for him to come outright and tell you all these things."
De Jong said her husband suffered harassment at work, while serving as a logistics officer aboard the supply ship HMCS Preserver.
One incident involved a drunk female officer who allegedly urinated on the floor of de Jong's cabin.
Maria de Jong said her husband became the butt of jokes after that incident. One superior officer, according to de Jong, told him, "Some men have to pay for that kind of service."
'I was flabbergasted'
She said someone posted a sign on his cabin door saying, 'Women's Head' — the nautical term for bathrooms.
"It's like, really? When Derek told me this I was flabbergasted," said de Jong.
She said her husband felt micromanaged and belittled by a superior officer. She said he also felt pressured to look the other way when financial accounting rules were not being followed. De Jong declined to provide any details about those allegations.
De Jong told CBC News her husband complained to his superiors on board, but nothing changed. She said he flew home from the ship to take his complaints up the chain of command and turned himself in as soon as he returned to Halifax.
"Derek said, 'You know what, we need to go straight to the base so I can report to the MP [military police] shack,'" she recalled.
De Jong said in the year and a half since her husband left HMCS Preserver, he has been working at CFB Halifax and has been praised for his work.
She said his complaints of harassment — as well as a letter she sent to the chief of defence staff — have been ignored.
The Department of National Defence told CBC News it won't comment while a case is before the military justice system.
'He's being made a scapegoat'
"They know what type of man he is, they know what kind of ethics he has. His work is impeccable," said de Jong.
"But those that can do something have basically put their head in the sand and said, 'Yup, let this happen. Just let it happen. Let's hang one man.'"
De Jong said her husband had a chance to plead guilty to the charge of being absent without leave in an informal summary process before the commander of CFB Halifax.
He was told his punishment could be as minor as a $1 fine.
De Jong said her husband was warned that if he chose a court martial, military prosecutors could pursue a stricter charge — such as desertion.
She said her husband elected a court martial so he could air his complaints in public.
"He's being made a scapegoat. What message are you really sending out by doing this then? On the one hand you're saying, 'Yes, report, report, report. We want to know. We want to change it, we want to change the culture of the navy,'" said de Jong.
"Yet when somebody does, this is what you do to them."