The accident involving HMCS Algonquin and HMCS Protecteur will "quite seriously compromise" the country's naval readiness on the West Coast, especially in light of continuing repairs to the frigate HMCS Winnipeg, rammed by an American fishing trawler in a separate accident last spring.
"This is a politically awkward time to be absent from the Pacific," said Dan Middlemiss, of Dalhousie University in Halifax, who has written extensively about the navy.
Naval engineers are conducting damage assessments on both the destroyer and supply ship, which have returned to their home port of Esquimalt, B.C., and have not said how long each vessel will be laid up.
Commodore Bob Auchterlonie, commander of the Pacific fleet, said the damage to Protecteur is "cosmetic" and the ship hopefully will be back at sea next week.
A more extensive damage survey will be carried out on Algonquin over the next few weeks.
Middlemiss says both the Harper government and the navy must decide whether the benefits of returning the 40-year-old destroyer to service outweigh the cost of retiring the ship, which has the capacity co-ordinate other Canadian warships when they operate as a task force.
Retirement would be a serious consideration, especially if repairs stretch out more than a year, Middlemiss said.
Auchterlonie wouldn't speculate on what might happen.
"We're only at the beginning of this extensive and thorough damage assessment," he said in an interview from Esquimalt.
"It's going to take some time. Once we have that information, based on that assessment, we'll consider the repair paths and the timeline to get her back to sea."
Documents obtained by The Canadian Press under access-to-information legislation show the navy anticipates Algonquin and her sister ships HMCS Iroquois and HMCS Athabaskan will retire over the next few years, possibly without replacements in the water.
A series of slides, prepared in 2011 for the now-retired commander of the navy, admiral Paul Maddison, show the navy has been anticipating a "capability gap" with its command destroyers, but was doing everything to move replacements forward.
That replacement program — known as the Canadian Single Class Surface Combatant — is part of the Harper government's $33-billion national shipbuilding strategy. The program remains in the concept stage and is not expected to begin delivering ships until the mid-2020s.
Middlemiss says the navy may consider moving one of the two Halifax-based destroyers to the West Coast.
Damage to the Protecteur, the navy's only West Coast-based supply ship, appears limited to the bow. Middlemiss said having it out of commission underlines the government's inability to deliver replacements ordered by the previous government — and the wisdom of having three replenishment vessels.
When the Liberals first proposed new joint support ships, the program was set to deliver three all-purpose vessels. But when shipyard proposals came in higher than the budget, the Harper government put the program on ice in 2008.
The program is now expected to deliver only two ships, perhaps in 2018.
"The navy is in a tough spot on the West Coast," said Middlemiss.
But Auchterlonie says once Protecteur is back in operation, the navy's ability to operate task forces, as opposed to single ships, will be enhanced, and newly refurbished Halifax-class frigates have command capabilities that can substitute for Algonquin.