The gap is the result of a bottleneck in the Harper government's national shipbuilding strategy because one of the yards where civilian-grade vessels are being built can only handle one major project at a time.
Officials were forced to choose between replacing the navy's 1960s vintage supply ships and the aging coast guard icebreaker Louis St. Laurent.
They chose the replenishment ships, which have been the subject of an on-again, off-again procurement process for nearly a decade.
The new joint support ships, based on a German design, will begin construction in late 2016 with a target of having them in service by 2019-20, almost two years later than the last estimate contained in last spring's federal budget.
The gap for the navy's supply ships, however, means Canadian warships will have to rely on other allies for fuel and ammunition when deployed overseas.
Officials, speaking on background because they weren't authorized to discuss the matter publicly, said Friday that's not unusual; allies have been called upon in the past whenever one of the existing ships — HMCS Preserver or HMCS Protecteur — was in drydock for repairs and upgrades.
In the meantime, one coast guard official said the icebreaker will remain in service until 2021-22, but it will require as much as $55 million in refits and upgrades to keep going over 10 years.
"We're really lucky the Louis St. Laurent is in as good condition as she is currently," the official said. "She has been well maintained over the years and we have invested in her."
Senior defence and public works officials overseeing the program recognized in 2011 soon after the companies were identified that SeaSpan Shipyards in Vancouver would face construction congestion, say documents released to The Canadian Press under the Access to Information Act.
They have been working since then to figure out a solution.
The roughly 500 pages of documents and briefings from the joint support ship project office also show that in 2008, military planners examined the option of buying replacements offshore.
The analysis showed that the navy could get its ships faster and likely about 10 per cent cheaper than by contracting with a Canadian yard.
The examination was done after the Harper government decided in the summer of 2008 to halt the first round of procurement — started under the Liberals — and to begin anew. Bids submitted during the first round came in dramatically higher than the government's budget envelope.
Officials acknowledged Friday that the decision to include the supply ships in the government's strategy has meant delays, but it will ultimately mean the military gets the ship it wants.
The cost of building in Canada, where shipyard labour rates are higher than competing nations, has been the subject of scrutiny. Analysts and internal reports have suggested the country is paying a steep premium per ship to support the industry.
Opposition New Democrats were quick on Friday to paint the decision as another procurement failure.
"Let's be clear: these critical shipbuilding projects are facing delays because of the Conservative decision to cancel the Joint Support Ship procurement process in 2008," NDP defence critic Jack Harris said in a statement.
"That restart means that the Canadian navy will now face a two-year gap in resupply capacity, during which time Canada will have to rely on allies for essential resupply capabilities. The Canadian navy's capacity to conduct independent marine operations during this period will be greatly reduced."
A recent report by the parliamentary budget office suggested that had the Conservatives stuck with the original program, the navy would already have its ships, and likely for less money than what they'll eventually pay.