The bill to refit of HMCS Windsor in Halifax is running millions more than anticipated, CBC News has learned. (CBC)

The cost to refit one of Canada's trouble-plagued submarines is skyrocketing, according to documents obtained under an access to information request by CBC News.

In the year 2010 alone, the Canadian navy spent $45 million on repairs to HMCS Windsor. It had budgeted to spend just $17 million, the documents show.

It appears that every system on the British-built submarine has major problems, according to the documents, including bad welds in the hull, broken torpedo tubes, a faulty rudder and tiles on the side of the sub that continually fall off.

The refit of the Windsor is also taking much longer to complete than anticipated, the documents show. The refit started in 2007 and was scheduled to be completed in 2009. However, the documents indicate the Windsor won't be fully operational until almost 2013.

Because the submarine has been in drydock in Halifax for so long, it has become a bird sanctuary. The navy spent thousands of dollars just trying to keep the pigeons from roosting in the vessel.

According to the documents, the navy's three other submarines — HMCS Chicoutimi, HMCS Victoria and HMCS Corner Brook — are not faring much better.

For example, since the navy took delivery of HMCS Victoria in 2000, it has only been in the water for just over 100 days. It has spent the rest of the time undergoing repairs in drydock in Esquimalt, B.C.

HMCS Chicoutimi caught fire off Scotland on its maiden voyage in 2004, resulting in the death of Lieut. Chris Saunders. It won't be ready for sea until about 2012.

The British Royal Navy launched the Upholder-class, diesel-powered submarines in the late 1980s and early 1990s before withdrawing them from service in 1994. Canada bought four of them from the British navy in 1998 for $891 million.

The deal was considered good at the time, but the fleet has been plagued with problems. There have been serious electrical problems as well as rust and general deterioration in the subs, which had sat mothballed in salt water for the previous four years.