Chief Petty Officer 2nd Class Gilles Duquette, 54, was found dead inside a base residence Tuesday morning when he failed to report for duty.
The 29-year-veteran with the Royal Canadian Navy transferred to CFB Esquimalt last March and was a member of its administration section.
Military police discovered his body after a search that was launched when he failed to report for duty.
Speaking for CFB Esquimalt, Capt. Jenn Jackson said Duquette's body was discovered Tuesday morning.
"I can tell you it's always devastating when we lose a service member and our condolences definitely go out to his family and friends," said Jackson.
Duquette was deployed to Syria in 1989 and Bahrain in 2002.
The military's National Investigation Service is working on the case instead of the Victoria Police Department, because the death occurred on National Defence property.
The BC Coroners service is also investigating, but has not released a cause of death.
Canada's Armed Forces have been rocked by several suicides over the past few months, including four in the space of just over a week at the end of November.
Last week, National Defence said it was in the process of hiring up to 54 mental health professionals to fill a decade-old need for supportive services.