The fire occurred Sept. 6 in Victoria, but was only reported this week, the Victoria Times-Colonist said.
Commanding officer Lt. Cmdr. Christopher Ellis told the newspaper no one was injured in the fire, as it happened inside the closed-off communication mast of the HMCS Victoria during a survey for radiation hazards.
Ellis said it would only be a matter of days to restore the damaged communications equipment and the sub's crew would resume training exercises soon. He told the newspaper he would prefer an electrical fire to happen while in port rather than at sea.
The diesel-powered sub is one of four Canada bought from Britain in 1998 and all four have been plagued with problems.
Three are based on Canada's west coast and the fourth on the east coast is so badly rusted it will likely be out of service until next year.
Another submarine is being refurbished after it caught fire in the Atlantic Ocean in 2004 on its way from Britain. One sailor was killed in that incident.
The fourth sub needs repairs after it hit the ocean floor in the northern Pacific Ocean and will be out of service until 2016, the report said.