Cmdr. Joshua Yanchus, who was the executive officer aboard HMCS Calgary, based in Esquimalt, B.C., was charged Monday by the military's criminal investigation branch.
The offences are alleged to have taken place aboard the frigate on June 25, 2014, while the warship was taking part in a major U.S.-led exercise in the Pacific.
Lt.-Cmdr. Mike Amirault, the deputy commander of the Canadian Forces National Investigation Service, said all members of the military are expected to conduct themselves in "an appropriate and professional manner at all times."
He said the charges are significant.
Last December, the commander of the Canadian navy ordered that sailors be banned from consuming alcohol aboard ships, unless the vessel is tied up or an exception has been made for a special occasion.
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