WASHINGTON–Proponents of an alternate engine for the Joint Strike Fighter are mounting an 11th hour lobbying effort to win fresh funding for the project, even as lawmakers in the lame-duck Congress prepare an austere budget.

Lobbyists for General Electric are working with top lawmakers on the House Armed Services Committee and other key panels to push for an amendment to a stop-gap funding bill that would add money for the competing JSF engine, manufactured by GE in partnership with Rolls Royce.

The JSF’s main engine is made by Pratt & Whitney. The two companies have been locked in a long and expensive lobbying battle over the JSF program. The Pentagon doesn’t want the alternate engine, but GE’s backers in Congress have kept the project alive.

But this latest development represents a new twist, with very high stakes, according to GE supporters. Their fear is that if Congress does not proactively include money for the alternate engine in its year-end spending bill, Defense Secretary Robert Gates could quietly kill the program.

The concerns stem from of a little-noticed Sept. 30 directive issued by the federal Office of Management and Budget. The OMB missive spells out how the Obama Administration will apportion money for existing federal programs if, as seems likely, Congress passes only a continuing resolution (CR), instead of a full-fledged budget, to keep the government running into next year.

A  CR would essentially nix the pending fiscal year 2011 appropriations measures that detail which federal programs get additional funding and which do not. The House passed a defense spending bill that includes money for the GE-Rolls Royce alternate engine. The Senate version does not.

The OMB directive suggests the White House could withhold funding for current programs in cases where Congress has sent a mixed message about its intent. “If either the House or Senate has reported or passed a bill that provides no funding for an account at the time the CR is enacted, this automatic apportionment does not apply,” the OMB bulletin states.

David Manke, a lobbyist for Pratt’s parent company, United Technologies Corp., said Department of Defense officials have indicated they have funding to take the alternative engine program through Dec. 3.

“After that it’s unclear,” he said of the program. “If there’s no authorization bill, it does give DOD a lot more leverage on what they could do. They could say, ‘We don’t have enough money to go around. We have higher priorities’.”

Adding to GE’s concerns is the fact that Gates has said he doesn’t want the alternate engine, and that the White House has threatened to veto a defense bill that includes funding for the program.

“There is significant activity underway on the Hill, in which key supporters of competing JSF engines are advocating an amendment to the CR language,” said Rick Kennedy, GE’s spokesman. “I couldn’t speculate on odds, but the supporters for competing JSF engines are being vocal.”

Jennifer Kohl, a spokeswoman for the House Armed Services Committee, declined to comment on the matter except to say: “The committee maintains that the second engine is important both to protect taxpayer dollars and to protect our national security.”

A spokesman for the House Appropriations Committee, which will craft any CR in that chamber, said no decisions have been made about the 2011 spending bills. He said lawmakers haven’t even settled on whether to draft a more comprehensive omnibus budget or opt for a CR.

But Republicans have voiced strong opposition to passing an omnibus budget, arguing that a lean-and-trim CR would send a message that Congress is serious about fiscal restraint. Whether it gets fattened up a little after Thanksgiving, with some special stuffing for GE, is uncertain.

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