Canada's only fully operational submarine is heading back to Canada after engine trouble, just months after another voyage was cut short by a different issue.

Halifax-based HMCS Windsor had a component in one of its two diesel engines malfunction Friday while off the Eastern Seaboard, the Department of National Defence said in a statement late Saturday afternoon.

HMCS Windsor has been plagued by problems in recent years. In March, the submarine was forced to return to Halifax after crew saw "a little bit of smoke" coming from a battery cell, Marine Forces Atlantic said at the time.

The federal government spent more than $266 million to repair, refit and maintain the submarine in recent years.

HMCS Windsor, one of Canada's Victoria-class submarines, performs sea trials in Halifax's Bedford Basin in this December 2012 file photo. (Andrew Vaughan/The Canadian Press)

'Prudent' to return

For this latest issue, the submarine will be inspected to determine the "degree of repair work" needed, the statement said.

HMCS Windsor engineers and technicians assessed the unspecified issue, fixing it enough to allow the submarine to travel back to Halifax on its own steam. A second system is working, but the military said it would be "prudent" to return the boat to Halifax until fully fixed.

HMCS Windsor is scheduled to join a Canadian-led operation in September. (Submitted by Maritime Forces Atlantic)

'Second to none'

Rear Admiral John Newton said in the statement he was proud of the submarine's teamwork.

"I congratulate them for their successful work-ups and share their disappointment in this machinery casualty," he said. "Their operational tempo has been second to none and they've performed admirably under demanding circumstances."

The submarine, with its crew of around 50 sailors, is scheduled to join the Canadian-led Exercise Cutlass Fury in September, the DND statement said.