"The president, the military services and I continue to oppose this extra engine," Gates said in testimony before the House Armed services Committee.
He spoke a few hours before a scheduled vote on the House floor to strip a spending bill of $450 million ticketed for production of the engine. The vote loomed as an early test for 87 GOP freshmen who confronted a choice between cutting spending and injecting competition into the F-35 program, the costliest weapons program in Defense Department history.
The money for the engine is included in a $1.2 trillion spending bill that would make deep cuts while wrapping up the unfinished business lawmakers inherited after last year's collapse of the budget process. That includes $1.03 trillion for agency operating budgets that need annual approval by Congress and $158 billion for military operations in Iraq and Afghanistan.
Like Obama, former President George W. Bush tried to kill the alternative engine, and their efforts have been supported by lawmakers from Connecticut, where the main F-35 fighter engine is built by Pratt & Whitney, as well members from Florida, Texas and other states.
Gates has said the engine would waste almost $3 billion over the next few years,
But the alternative engine has its own supporters, including Speaker John Boehner, R-0hio. The alternative engine would be built by the General Electric Co. and Rolls-Royce in Ohio, Indiana and other states.
"We have to step forward, we have to cut back on areas, and this is an area that the secretary of defense said we need to cut back on," freshman Rep. Bob Dold, R-Ill., said Tuesday night in debate over the proposal.
The engine battle divides along regional rather than party lines, in contrast to the partisan warfare on the underlying bill, which sharply cuts domestic programs and foreign aid and earned a veto threat from the White House budget office and a warning from President Barack Obama against unwise cuts "that could endanger the recovery."
The House worked through the night into early Wednesday; debate on the bill is expected to take all week. A frosty reception awaits the bill in the Democratic-controlled Senate, which won't take up its version until next month. So it'll require passage of a separate short-term government funding bill by March 4 to prevent a government shutdown that neither side says it wants.
The GOP bill, separate from the 2012 budget Obama unveiled on Monday, covers spending for the fiscal year that ends Sept. 30.
The GOP legislation would make sweeping cuts to domestic programs ranging from education and science to agriculture and the Peace Corps. It slashes the Environmental Protection Agency, a favorite target of Republicans, by 29 percent from last year's levels, and would eliminate federal funding for public broadcasting, the AmeriCorps national service program, police hiring grants and family planning programs unpopular with conservatives.
The Food and Drug Administration budget would decline by 10 percent, and spending also would fall by 10 percent for a food program for pregnant women and mothers and their children.
The cuts are all the more dramatic because they would be shoehorned into the last half of the budget year that started Oct. 1.
The bill marks the first significant attack on federal deficits by Republicans elected last fall with the support of smaller-government tea party activists.
The measure came to the floor just a day after Obama unveiled his budget for next year and is merely a first round in what looms as a politically defining struggle that soon will expand to encompass Social Security, Medicare and Medicaid, the massive government programs that provide benefits directly to tens of millions of people.
"We know we can't balance this budget simply by reducing nonsecurity, nondefense spending," said Rep. Mike Simpson, R-Idaho, referring to the 359-page bill that would cut $61 billion from domestic programs.
The measure is sweeping in its scope, cutting spending from literally hundreds of domestic budget accounts and eliminating many others. At the same time, the Pentagon budget would be increased by almost 2 percent from current levels.
In a reflection of tea party priorities, the practice in which lawmakers direct money to their pet projects is banned in the bill. And in a fulfillment of a promise that Republicans made to the voters last fall, about $100 billion would be cut from funds that Obama requested for the current fiscal year.
At a White House news conference, Obama said he looked forward to working with lawmakers in both parties on the spending bill, but warned against "a series of symbolic cuts this year that could endanger the (economic) recovery."
A few hours after Obama spoke, the White House issued a formal statement expressing "strong opposition" to the legislation for "cuts that would sharply undermine core government functions and investments key to economic growth and job creation."
Republicans used their first major spending bill to reflect conservative priorities on a range of issues, from abortion to the environment.
The bill would prohibit federal funding for any private organization that uses its own funds to facilitate abortions, except in cases of rape, incest or when the life of the mother is in jeopardy.
At the same time, the EPA would be barred from regulating greenhouse gas emissions from factories and other stationary sites.
Conservatives said they would attempt to add other policy requirements to the legislation during floor debate, including one to prevent the implementation of the year-old health care law.
Others are backed by affected industries. One would stop the Federal Communications Commission from enforcing its proposed new "network neutrality" policy, which prohibits phone and cable companies from interfering with traffic on their broadband networks.
Officials said Senate Democrats agreed in a closed door meeting during the day to support one element of Obama's budget, a call for a five-year freeze across hundreds of domestic programs. Some accounts would face cuts to allow for growth in others. A formal announcement is expected Wednesday.