The Centre for Policy Alternatives and the Rideau Institute estimate the current numbers for the F-35 could be off by between $12 billion and $81 billion, depending on a variety of factors and risks over 40 years.
An independent analysis of the program, conducted by the Public Works secretariat overseeing the plan to replace Canada's CF-18s, pegged the total lifetime cost of owning 65 stealth fighters at just over $44 billion over four decades.
Michael Byers, a University of British Columbia professor and defence expert, says his estimate would be on top of that.
Byers says he questions the math in the secretariat's report because it bases its long-term maintenance on data numbers from the existing fighters.
He says the F-35 is still under development, but it has already proven that its operating and maintenance costs are about 1.5 times higher than the CF-18s.
Byers says the figures are significant because the Harper government is close to deciding whether to stick with the troubled F-35 program or open up the CF-18 replacement to competition.
A National Defence estimate on the long-term operating costs of the F-35 will be among the pile of reports cabinet is expected to consider.
Byers says his numbers, which project the total cost could reach $126 billion, are based on figures coming out of the U.S. Government Accountability Office in Washington, which has tracked the program extensively.
He also says other structural costs, such as modifying the air force's tanker fleet to operate with the F-35, are not included in the secretariat's public estimates.
The research done by Byers also examines risks such as volatile fuel prices, inflation and a fluctuating exchange rate.
He says a one per cent increase in the rate of inflation would add $5 billion to the overall price tag.
The air force has already publicly suggested that in order to keep costs down, it will fly the F-35 less often than the CF-18s, cutting 4,000 flying hours per year out of its training plan and using simulators more often.
But parking the jets simply creates a false economy, Byers says.
The Harper government signalled in 2010 that it intended to buy the F-35, but a set of scathing reports — including one by the auditor general — accused both National Defence and Public Works of not doing their homework and deliberately low-balling the cost.
The program was put on hold in December 2012.