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Associate Defence Minister Julian Fantino delivers a speech in Ottawa on March 16, 2012.Adrian Wyld

The Harper government was privately concerned last fall about costs, delays and the quality of communication it was receiving on the U.S. F-35 stealth fighter project even as its chief spokesman on the file assured Canadians all was well.

Ottawa dispatched associate defence minister Julian Fantino to Fort Worth, Tex., to register its concerns about the F-35 Lightning – a trip Mr. Fantino took in early November, 2011, in his role as the government's point man on military procurement.

A Sept. 30, 2011, National Defence briefing note, obtained under access to information law, indicates the Conservatives wanted to use the visit to Texas to register their unease with how the project was unfolding, while assuring the Americans they were still solidly supportive of the Joint Strike Fighter (JSF) program.

It would be another six months before the Conservatives publicly acknowledged the problems with the F-35 procurement – after a damaging report from the Auditor-General – and froze spending on the program while carrying out an independent review of its costs and benefits.

The September, 2011, briefing note was signed by deputy defence minister Robert Fonberg.

"The purpose of this trip is to demonstrate the government's commitment to the JSF program, while impressing upon key interlocutors Canadian concerns with cost, production schedules and the need for transparent communication to JSF partner nations," the note said.

Even while Canada harboured private apprehension about how the program was proceeding, Mr. Fantino was publicly rejecting the notion there was reason to be concerned about the acquisition of fighters that would replace Canada's aging CF-18 Hornets.

"Our budget for the purchase of F-35s remains on track," Mr. Fantino told the Commons on Oct. 5, 2011.

His message continued unchanged through the November meetings in Fort Worth, where F-35 manufacturer Lockheed Martin has a plant.

"We will purchase the F-35," Mr. Fantino told Fort Worth business leaders during his visit. "We're on record. We're part of the crusade. We're not backing down," the Fort Worth Star-Telegram reported him saying.

The development of the F-35 Lightning has been riddled with cost overruns and technical problems – much of it out of Canada's hands because the project is being run by the U.S. government. The Conservatives for a long time insisted the planes would cost $75-million each, but the Pentagon estimates the price tag at about $135-million.

About a week after he returned from Fort Worth, Mr. Fantino was as bullish as ever, assuring the Commons "our program is on track and on time."

The government continued defending the F-35 until March 12, 2012, when Mr. Fantino oversaw an abrupt reversal of messaging. At that point, he acknowledged, Ottawa could still back out of the program.

Back on March 12, Mr. Fantino repeatedly used the word "if" when referring to buying the F-35s. Although he maintained the government is still convinced the planes are the best available, he added: "But we have not as yet discounted the possibility, of course, [of]backing out of the program."

The change seemed to be part of an elaborate strategy to set the stage for the April 3 Auditor-General report, which was already circulating inside the government.

Appearing in front of the Commons public accounts committee on Thursday, Auditor-General Michael Ferguson expanded on his concerns over Ottawa's failure to reveal the full costs of the F-35 program over the jets' entire 36-year lifespan.

He said costly upgrades to the aircraft must be factored in when the program's full budget is restated, as well as the need to replace some jets in the case of accidents.

"There were some significant things that were missing from the life-cycle costing in this, for example, attrition, for example, upgrades, and the fact that these aircraft were going to last for 36 years, not just 20 years," Mr. Ferguson told MPs.

"When we raised the issue of life-cycle costing and the fact that it was not complete, I don't believe that we were nitpicking in any way. We were saying that there were significant elements that were missing," he said.

The issue of cost is a sensitive one for the Conservatives, who want to ensure that the F-35 file does not taint their reputation as strong fiscal managers.

Conservative MP Laurie Hawn said in committee that the only definitive number at this point is the $9-billion that has been set aside to buy new fighter jets, explaining that everything else – such as maintenance and operating costs – "is an estimate."

Despite the controversy, the Auditor-General said everything still indicates the government still intends to replace the CF-18s with F-35s toward the end of the decade. However, he said the new secretariat tasked with overseeing the process could receive a clear direction to consider other aircraft to replace the existing fighter jets.

Still, Mr. Ferguson said the secretariat would need to come up with mitigation measures to level the playing field for all other manufacturers in the event of full competition.