HMCS Windsor was lowered into Halifax harbour Wednesday after spending five years in dry dock for an extensive refit that cost $45 million in 2010 alone.

The launch began in the morning. The process took several hours as a Syncrolift lowered the submarine slowly into the water.

Divers assessed the position of the propeller once it was fully submerged. After that, two tugboats attached lines to the sub and moved it from the cradle to a nearby dock.

The sub will remain there until maintenance crews determine that it is water tight and that all systems are functioning. It's expected to undergo sea trials this year and be fully operational next year.

HMCS Windsor is one of four British-built submarines purchased in 1998. A refit dragged on past 2009, pushing the repair bill in 2010 from a budgeted $17 million to $45 million.

Former naval officer Ken Hansen said the clock is running to get HMCS Windsor and the other troubled submarines into the water.

"The navy needs to prove that it can actually administer and successfully manage this program," he told CBC News on Tuesday.

"If the problems of the past continue to manifest themselves, the government will lose patience and Canada, I believe, will be out of the submarine game forever."

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There have been serious electrical problems, as well as rust and general deterioration in the subs, which had sat mothballed in salt water before Canada bought them.

Defence Minister Peter MacKay said it would be another couple of years before all four submarines are fully operational.

HMCS Victoria, based on the West Coast, successfully test-fired torpedoes last month.

But neither HMCS Corner Brook nor HMCS Chicoutimi is ready for service yet.