The HMCS Algonquin and HMCS Protecteur were conducting close-quarters towing exercises Friday morning when the accident occurred, the navy said in a statement.
The Algonquin sustained significant damage to its hangar and will no longer be deployed to the Asia Pacific region. The Protecteur's bow was damaged to a lesser degree.
The damaged ships were expected to reach port in Esquimalt, British Columbia, by late afternoon, CTV News reported. No injuries were reported.
The navy said the collision would be investigated and a Board of Inquiries would issue recommendations on how to prevent similar accidents in the future.
"The Royal Canadian Navy will be conducting an investigation into this unfortunate incident in order to determine exactly what happened," Commodore Bob Auchterlonie, commander of Canadian Fleet Pacific, said in a statement released by the Department of National Defense.