The incremental cost of Canada's mission in Libya last year was double the $50 million estimate Defence Minister Peter MacKay gave last October, a new document shows, but a top Canadian general says the military's estimate was accurate.

The report was tabled in the House of Commons this week after the discrepancy was discovered by the Rideau Institute, a non-profit think-tank, which stated in a release Friday that MacKay wasn't reporting the actual costs.

The mission was extended one month and officially ended Oct. 31, 2011.

Figures released in the government's Report on Plans and Priorities show the cost of the Libya mission was $103.6 million. The full cost of the mission was $347 million.

That increased figure comes from the Defence Department's accounting practice of reporting only "incremental costs" -- expenses considered above and beyond normal operating expenses.

The institute said about 15 per cent of that increase can be attributed to the one-month extension, but it's still about $30 million above MacKay's estimate.

"As in the F-35 stealth fighter fiasco, it seems that Defence Minister Peter MacKay was low-balling the true costs of the Libya operation at the time," said Steven Staples, president of the institute in the release.

But Major-General Jonathan Vance denied there was any discrepancy.

"With respect to the cost of Operation Mobile, Canada's mission in Libya, I can say with complete confidence that the department has been utterly transparent with Canadians, members of the media and Parliament as to the costs of the missions both as they evolved and in their estimates," Vance said in a press conference Friday.

According to Vance, as of Jan. 31, total incremental expenditures incurred for the mission were estimated at $106 million, but actually came to $103.6 million.

"This is the formal record of additional expenses to DND and Canadians for conducting the mission. All other figures, including the full cost figure of 347.5 million, include money that would have been spent whether the mission was performed or not," he said. "This includes costs of salary, depreciation of equipment, command and control, and so on."

Vance did not speculate on why MacKay gave the lower estimate in October, although he acknowledged that the defence minister would have been aware of DND's estimate, The Canadian Press reports

The institute had said as early as June the true incremental cost of the mission would be millions more than the government projected, a fact MacKay disputed at the time.

During question period in the House of Commons on Friday MacKay said, "These expenditures to October 13 were accurate, were correct, there were further costs incurred of course…and as we have seen, twisted logic tells us that they were withheld by table."

While the government may not be misleading the public when if comes to military expenditures, "there is such a reluctance to share these numbers or to put them out in anything even resembling a pre-packaged form that makes any sort of independent analysis virtually impossible," Rob Huebert of the Canadian Defence and Foreign Affairs Institute, told CTV's Power Play on Friday.

Questions about the mission's true cost come on the heels of the F-35 jet purchase debacle, in which the jets were eventually reported to be $25 billion, not $15 billion.

"They're two different things (F-35) but they both have an optics problem for the Conservatives," CTV's Mercedes Stephenson told CTV's News Channel Friday.

But David Perry, an analyst with the Conference of Defence Associations Institute, suggested the F-35 controversy may stem more from a communications issue within the government.

"I think the government is unfortunately taking a bit of a hit for a project that I don't actually think is in as bad shape as has been portrayed publicly," he said on Power Play. "They've not been able to actually speak to this issue in a way that accurately captures the state of the project itself."