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Lieutenant Derek De Jong sits with his wife, Maria, in a coffee shop during his court-martial in Halifax on May 7, 2014.ANDREW VAUGHAN/The Canadian Press

Claiming harassment and bullying, including by a female colleague who urinated on his cabin floor, Royal Canadian Navy officer Derek de Jong said he'd had enough.

He jumped ship, leaving his supply vessel, HMCS Preserver, in Key West, Fla., in September, 2012. At his court martial this week, he pleaded guilty to desertion and, on Wednesday, was fined $5,000 and given a severe reprimand.

But just hours after he was disciplined, his superiors announced they are launching an investigation into his claims.

"I am here to tell you that some of the allegations made by Lieutenant de Jong concern the navy," Commodore Scott Bishop, who commands all the ships in the Atlantic fleet, said Wednesday in a quickly arranged scrum. "There will be a formal investigation that will look at the entirety of the issue with the intent of figuring out exactly what is at the bottom of Lt. de Jong's allegations."

Cmdre. Bishop said he doesn't believe there is a "culture of harassment" in the navy, and added he is confident that all the systems are in place for people to report when "they're in a situation they are finding personally difficult." He said the first he heard of Lt. de Jong's allegations was "after he had left the ship."

According to documents from the court martial, the day he deserted Lt. de Jong had informed his commanding officer that he had a "toxic working relationship" with another of the ship's officers.

Lt. de Jong's wife, Maria, has talked strongly about the harassment she believes her husband encountered. "It had to be done. Somebody had to do it," she said of her outspoken response. Nothing like this had ever happened before to her husband, she said in an interview, describing him as a man who has "very strong ethics and morals."

"That's what we teach our kids as well," she said about their two girls, 10 and eight. "With the whole bullying thing, it's a big topic at school. And we always tell them … always treat [other people] the way you want to be treated. Respect, respect, respect – that is a very key word in our household."

Ms. de Jong said she and her husband are very close, and that he e-mailed or called her during the time he was away on his ship, where he served as a logistics officer trainee. He told her about the incident with his female colleague. "I felt violated," she said, "because it happened to him, it happened to us. What happened to respect? What happened to dignity? How can any individual do this?"

After the incident, Lt. de Jong was ridiculed. He testified that one of his superior officers told him that "some men have to pay for that kind of service." He said he reported that to the commanding officer.

Ms. de Jong said she knew he was under a lot of "stress," and on the day he deserted she said she "tried to calm him down."

"I tried to say, 'You know what, honey, calm down, let it go, let's see if we can work through this.'"

For nearly two years, the family has been under a lot of pressure as Lt. de Jong faced the possibility of a much more severe sentence, including imprisonment. Outside court Wednesday, he said his sentence was "fair" and that he had assumed the penalty would be more.

"As the judge said, I'm being given a second chance. I hope I can re-earn the respect of those appointed under me," he said.

Lt. de Jong has filed a grievance, which Cmdre. Bishop said is "working its way through the system." He said "some remedial measures" were taken against the offending officer. He won't say what they were, although this officer is still serving in the navy.

Ms. de Jong, meanwhile, said she is not a "vindictive sort of person," but added: "I really hope they pay for what they did."

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