The Navy’s top officer said Tuesday he opposes the continued development of an alternative engine for the new F-35 Joint Strike Fighter jet, a program at the center of a veto clash between the White House and Congress.

At issue is whether to buy only Pratt & Whitney engines for the F-35, a jet to be flown by all U.S. military services and several allies, or to continue developing and ultimately purchase an additional back-up engine made by General Electric Company and Rolls Royce.

Congress launched the second-engine program in 1997 and has appropriated $2.5 billion for it since. For the last three years, however, the Pentagon has tried to kill the initiative. Yet Congress has resisted each time by appropriating money for the backup program.

Despite the official opposition of both the Bush and Obama administrations to the second engine, some military leaders have worried about relying completely on a single engine manufacturer. But in a brief interview Tuesday, the chief of naval operations, Adm. Gary Roughead, weighed in on the debate, arguing that keeping parts for two engines on the decks of aircraft carriers was not advisable.

“Space is at a premium,” he said. “Therefore you can put me solidly in the one-engine camp.”

Roughead’s opposition to the second engine could fortify the administration’s case. But if President Obama is to end the program, he will first have to convince key lawmakers to change their minds.

The defense authorization bill (HR 2647) that the House passed June 25 would endorse spending $603 million to develop and procure the second engine. The Senate Armed Services Committee approved its own draft of the bill the same day, which would include $439 million for the second engine. The House bill would require the Pentagon to request funding for the second engine in the future. In addition, the legislation would limit the military’s ability to spend any more than 75 percent of the overall F-35 development funds unless it spends all the money appropriated in fiscal 2010 for the second engine.

White House Threat

In a June 24 Statement of Administration Policy, the White House said it “strongly objects” to the authorization of the funding and the requirement that money be requested in the future because doing so would “delay the fielding of the Joint Strike Fighter (JSF) capability and capacity, adversely impacting the department’s overall strike fighter inventory.” The White House also opposed the proposed limit on how much the Pentagon could obligate for the overall program.

However, the administration conditioned the veto threat on the determination that the provisions would have a significant, adverse impact on the overall F-35 program.

“If the final bill presented to the president would seriously disrupt the F-35 program, the president’s senior advisors would recommend a veto,” the Office of Management and Budget statement said.

It remains to be seen whether the administration would issue the same threat if either of the more important defense appropriations bills, which have yet to be written, contain similar provisions.

In announcing his fiscal 2010 budget request in May, Obama cited his plan to end the second engine program as a way to “save money by eliminating unnecessary defense programs that do nothing to keep us safe.”