WASHINGTON–Defense Secretary Robert Gates said Monday that he would use “all available legal options” to kill the alternate engine for the Joint Strike Fighter, unless Congress moves definitively to save the program in the next few weeks.

Gates called the extra engine, in development by General Electric and Rolls Royce, “an unnecessary and extravagant expense, particular during this period of fiscal contraction.” Continuing the program, he said, “would be a waste of nearly $3 billion… and the money is needed for higher priority defense efforts.”

Gates’ remarks give a major boost to Connecticut-based Pratt & Whitney, which makes the main engine for the JSF, in its years-long effort to beat back competition from the GE-Rolls partnership.

Gates made his comments as Congress girds for another major legislative tussle over this issue. House Republicans have crafted a spending bill for the rest of fiscal year 2011 that includes $450 million for the GE-Rolls alternate engine.

GE and Rolls Royce are lobbying aggressively to protect that funding, while Pratt & Whitney, along with its parent company United Technologies Corp., is pushing to strip it out.

The battle is likely to come to a head in the next few days. Rep. John Larson, D-1st District, and others plan to propose an amendment that would remove the $450 million alternate engine funding from the broader spending bill.

In an interview last week, Larson called the alternate engine a “boondoggle.” House Republicans should cut funding for that before they take their budget axe to other vital domestic programs, such as low-income home energy assistance, Larson said.

Since 2006, Pentagon officials have said they no longer wanted the GE-Rolls Royce fall-back engine, arguing the Pratt model was on track and it was a waste of money to build both.

But Congress has repeatedly ignored DOD’s request, agreeing with GE’s pitch that maintaining competition in the JSF program would keep costs down over the long term. The new House GOP majority, including Speaker John Boehner, R-Ohio, and Eric Cantor, R-Va., have been particularly supportive of GE’s position. Both their home states would benefit if the alternate engine is preserved, since GE has a plant in Ohio and Rolls Royce has a facility in Virginia.

Given that Boehner and Cantor now control the House, Larson, the House Democratic Caucus chair, conceded that his amendment faces an uphill battle.  Even during the last Congress, when his party held a sizeable majority, Larson was unable to win House passage of a similar provision nixing the extra engine funding.

The best case scenario for opponents of the alternate engine is if Congress deadlocks over the funding bill. A stop-gap measure now in place to keep the government running is set to expire on March 4.

Gates, in his comments on Monday, noted that while the House has voted for continued funding for the alternate engine, the Senate has not. And he signaled he would make the final call on the program himself if lawmakers failed to do so.

“The Congress has not spoken with one voice on this matter and the department has been operating this fiscal year under ambiguous guidance at best,” he said.

Until now, he said, “I decided to continue funding the JSF extra engine on a month to month basis,” so Congress could resolve the matter.

But that has cost taxpayers $28 million a month “for an excessive and a unjustified program that is slated for termination,” Gates said. So “when the current continuing resolution expires, I will look at all available legal options to close down this program.”

Gates declined to elaborate on what his options are. “My hope is, quite frankly, that there will be a debate about this on the floor of the House this week and that members will address this directly,” he said. “And my hope is that particularly the new members who are interested in fiscal responsibility will see this as an opportunity to save $3 billion for the taxpayers that can be put to better use.”

Even as Pratt supporters cheered Gates’ comments, GE signaled it was undeterred. Company spokesman Rick Kennedy said he, too, hopes the issue will be settled on the House floor, where he predicted the GE-Rolls forces would win. And he took issue with Gates’ characterization of the program.

“He claimed the F136 engine program would cost $3 billion to complete–a figure already discredited by the Government Accountability Office,” Kennedy said, adding that GE puts the number “closer to $1.8 billion.”

Kennedy criticized Pratt’s engine, saying it has been subject to cost overruns and other problems.

“There needs to be a debate on whether to hand a $100 billion monopoly of a single engine supplier whose costs are out of control,” Kennedy said. “Fifteen years of bi-partisan Congressional support for the F136 engine is based on good government policy that will save taxpayers money.”

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