Pentagon leaders made clear yesterday the F-35 Joint Strike Fighter is under continued scrutiny, expressing doubt about buying all three aircraft variants as well as attempts to revive the jet’s contested alternate engine.

Defense Secretary Leon Panetta and Chairman of the Joint Chiefs of Staff Army Gen. Martin Dempsey shared these view when fielding a wide array of weapon-system questions during their first hearing before the House Armed Services Committee (HASC). The hearing came as the panel and the Senate Armed Services Committee (SASC) reaffirmed their opposition to additional defense budget reductions to a federal-deficit-cutting committee.

Dempsey said he does not know if the Pentagon can afford to buy different variants of Lockheed Martin’s [LMT] F-35 for the Air Force, Navy, and Marine Corps.

Robert Gates, the former defense secretary, placed the Marine Corps’ F-35B short-takeoff/vertical-landing (STOVL) variant on probation earlier this year following technological challenges. Marine Commandant Gen. James Amos, though, has been outspoken in his support of the STOVL aircraft that has been undergoing sea trials.

“I am concerned about the three variants, whether as we go forward in this fiscal environment, whether we can afford all three,” Dempsey said under questioning from HASC member Rep. Jeff Miller (R-Fla.). “But I am eager to learn more about that. And I do have great respect for Gen. Amos’ judgment. But I’ll tell you that’s something we have to keep an eye on. (Having) three variants creates some fiscal challenges for us.”

Still, Dempsey said he is “supportive without caveat” of the development of the F-35, a fifth-generation stealth jet fighter. Panetta similarly said the aircraft is “something we absolutely need, it’s a remarkable plane, and it really does the job well.”

Regarding the F-35B, the defense secretary said he wants to ensure the aircraft goes through testing and any issues are resolved, so that “once it goes into production, (it) is going to be something that will be totally effective and will be totally capable of serving the mission that it’s required to do.”

“And if it performs well (in testing) then obviously it’ll be able to make the grade,” Panetta said.

Rep. Roscoe Bartlett (R-Md.), chairman of the HASC’s Tactical Air and Land Forces subcommittee, also quizzed the Pentagon officials on the proposal by the contractor building the F-35 alternate engine, a General Electric [GE]-Rolls-Royce team, to self-fund the development of the ill-fated F136 program.

The Pentagon has maintained the second-engine program is unneeded and too expensive, and terminated it in April shortly after Congress killed FY ‘11 funding for it. Yet supportive lawmakers, including Bartlett, have noted continuing the F136 may cost the Pentagon the same over the long term as continuing with just one F-35 engine. The General Electric-Rolls-Royce team offered to spend its own money to continue developing the alternate engine, which the House-passed FY ‘12 defense authorization bill would allow.

Bartlett asked how the Pentagon’s resistance to the self-funding scheme jibes with Panetta’s pledge support of competition with procurements.

Panetta said he does not want competitions to cost more money, and said people who have studied the matter maintain developing a second engine would cost more than not having it. When Bartlett responded that the Government Accountability Office has found continuing with two engines could save money, Panetta acknowledged that “frankly it’s disputed within the (Defense) Department and I’ve got to work through that.”

Panetta repeated the pledge now-Deputy Defense Secretary Ashton Carter made last month that Pentagon officials will meet with General Electric-Rolls-Royce about its self-funding proposal.

“I think we need to look at it to determine whether that is cost efficient,” Panetta told the HASC yesterday. “If in the end it’s going to cost me more money that’s not what I call good competition. If in the end it saves money then I’m willing to look at it.”

Panetta, meanwhile, called on the HASC during yesterday’s hearing to “do everything possible” to prevent further defense budget cuts beyond the $450 billion taken from the Pentagon’s 10-year plans by the Budget Control Act of 2011. HASC leaders sent letters yesterday to the Joint Select Committee on Deficit Reduction, which is weighing additional federal budget cuts, calling for the Pentagon to be spared further reductions. The SASC leaders were preparing similar letters.

Panetta also announced during the hearing he directed the Pentagon to speed up the process of having its financial statements ready to be audited, and “cut in half the time it will take to achieve audit readiness for the Statement of Budgetary Resources,” which he said would ensure that in 2014 “we will have the ability to conduct a full budget audit.”

He said he directed Pentagon Comptroller Robert Hale to revise the current plan “within 60 days to meet these new goals, and still achieve the requirement of overall audit readiness by 2017.”

Lawmakers often lament that the Pentagon’s books cannot be audited. A group of senators has called on the Government Accountability Office to assess the DoD’s audit preparedness. The HASC also formed a special panel in July that is assessing the Pentagon’s Financial Improvement and Audit Readiness plan.

Panetta said in a written statement he directed “increased emphasis on accountability and a full review of the (Defense) Department’s financial controls,” with “improvements put in place where needed.”