Defence planners expressed concerns about maintenance costs a year after the Conservatives signalled they wanted the jet, the documents show.
Internal briefings released under the Access to Information Act show air force officials worried in 2011 about the project's "affordability," and the impact on future operation, maintenance and national procurement budgets.
The Harper government announced in 2010 it had selected the F-35 as the country's next manned fighter.
More than 1,120 pages of documents, obtained by The Canadian Press, highlight concerns about the radar-evading jet and its potential impact on both the military and the federal treasury.
Retired air force colonel Paul Maillet, a critic of the F-35 program, said he was surprised by several aspects of the briefings, describing the sustainment plan as a potential "rabbit hole for money."
The government put the project on hold last fall and launched a market analysis of other fighter jets, but the F-35 remains a contender.
A spokeswoman for Public Works Minister Rona Ambrose emphasized no decision has been made, and that promises made in the aftermath of last year's scathing auditor general's report are being implemented.
"No money has been spent on the purchase of new fighter aircraft and we will not purchase a replacement aircraft until our seven-point plan is complete," Amber Irwin said in an email Tuesday.
A 2011 slide-deck presentation by the F-35 project's sustainment manager noted long-term affordability was an "issue," and that a "bow wave" of higher costs was expected when the jet entered service, then expected between 2016 and 2020.
The stealth fighter is still in development and the system of spare parts and weapons delivery will be globally operated and under the control of the U.S., Maillet noted.
"I would not be comforted by this model that they have here," he said. "It really, really gives them (the U.S.) a lot of control over our defence capability."
Unlike previous military aircraft, there will be no mid-life upgrade on the F-35s. Rather, the jets, which are largely run by computer will receive regular software and hardware upgrades in a system known as blocks.
Because there are several partners, each country will have to pay into a collective pool for those computer upgrades, something that will be expensive, Maillet said, especially if Canada wants specific features such as those dealing with Arctic operations.
"We have no idea how much these block upgrades are going to cost," he said.
"Canada will have to participate in the sustainment and upgrade over the life of the airplane and presumably of all the owners. ...
"These are phenomenally expensive things you are being asked to commit to without any idea what is it going to cost."
The auditor general in an explosive report released last year said Defence didn't have a handle on sustainment costs and that planners were still developing their assumptions for operating the fleet.
In testimony before a Parliamentary committee last year, the former top civilian at National Defence insisted sustainability wasn't an issue and that the stealth fighter would cost the same to fly and maintain as the existing squadrons of nearly 30-year-old CF-18s.
But the documents show that at least a year before Robert Fonberg's testimony and the auditor's report, the project planners had not only identified the issue as a major consideration, but warned of a "significant funding shortfall" related to base infrastructure.
When asked about the contradiction, a Public Works official would only point to what was written on the Defence Department website, noting that the next version of the F-35's long-term budget will be submitted to the federal Treasury Board this year.
"The estimated sustainment cost for the F-35A is also affordable within the department's long-term budget prorated over the entire life cycle of the fleet," says the website.
"To the extent that the sustainment costs could rise beyond the department's long-term budget, despite the substantial contingency allowances built into the estimate, the department will manage pressures through adjustments to the use of the aircraft and/or adjustments to the long-term budget."
That means the radar-evading jets would be flown less often compared with the CF-18s.