The surprise 230-195 defeat came at the hands of Democrats and tea party Republicans.
Democrats were opposed because the measure contains $1.5 billion in cuts to a government loan program to help car companies build fuel-efficient vehicles. For their part, many GOP conservatives felt the underlying bill permits spending at too high a rate.
The outcome sends House Speaker John Boehner, R-Ohio, and his leadership team back to the drawing board as they seek to make sure the government doesn't shut down on Sept. 30, the end of this fiscal year. It also raises the possibility that the government's main disaster relief program could run out of money early next week for victims of Hurricane Irene and other disasters.
Earlier Wednesday, Rep. Eric Cantor of Virginia, the No. 2 Republican in the House, had confidently predicted the measure would pass. Now, GOP leaders are scrambling to revive the measure on Thursday in hopes of wrapping up a final compromise with the Senate by the weekend. A rare weekend session is possible.
One option is to find a different spending cut to offset $1 billion worth of immediate disaster aid needed to make sure victims aren't cut off next week.
The Federal Emergency Management Agency has only a few days' worth of aid remaining in its disaster relief fund, lawmakers said. The agency already has held up thousands of longer-term rebuilding projects - repairs to sewer systems, parks, roads and bridges, for example - to conserve money to provide emergency relief to victims of recent disasters.
The looming shortage has been apparent for months, and the Obama White House was slow to request additional money.
The White House, a vigorous advocate of greater fuel efficiency for U.S.-made cars, welcomed the result of Wednesday's vote.
"We are pleased that the House of Representatives today rejected efforts to put politics above the needs of communities impacted by disasters," the White House communications director, Dan Pfeiffer, announced on his Twitter account. The White House had earlier declined to issue an official statement evaluating the measure, as is typical.
The underlying stopgap funding measure would finance the government through Nov. 18 to give lawmakers more time to try to reach agreement on the 12 unfinished spending bills needed to run government agencies on a day-to-day basis for the 2012 budget year.
Forty-eight Republican broke with GOP leaders on the vote; six Democrats voted for the measure. Some of the Republicans also came from manufacturing states like Michigan, which benefit from the loan program.
The measure was originally designed by GOP leaders to pass with bipartisan support. Last week, Democratic Whip Steny Hoyer of Maryland and Rep. Norm Dicks of Washington, the top Democrat on the House Appropriations Committee, said publicly that they would vote for it reluctantly.
The underlying stopgap measure was opposed by conservative Republicans unhappy with the spending rates set by the measure, which are line with levels set by last month's budget and debt pact with President Barack Obama. That measure provides about 2 percent more money for Cabinet agency budgets than Republicans proposed when passing a nonbinding budget plan in April. More than 50 Republicans recently wrote to Boehner calling on him to stick to the earlier GOP budget.
"This bill was designed to pass with Democrat votes, in part based on assurances from Reps. Dicks and Hoyer," said Erica Elliott, spokeswoman for GOP Whip Kevin McCarthy of California.
"Frankly, it's shocking as many Republicans voted for it as did."
Senate Democrats, who muscled through a stand-alone $6.9 billion disaster aid measure last week, called upon House GOP leaders to add additional disaster funding to whatever future stopgap measure rises from the rubble of Wednesday's vote. Unless Congress passes stopgap legislation by midnight on Sept. 30, much of the government will shut down.
"Consider making the disaster relief more robust" in the next bill, said Sen. Mary Landrieu, D-La. "Please talk to the Democrats."
Landrieu said FEMA Director Craig Fugate told her Wednesday that the agency's disaster relief fund may run dry on Tuesday. That would mean that there's no money to provide shelter, cash assistance or other help to victims of Irene, thousands of fires across Texas and northeastern states flooded by Tropical Storm Lee.
In the House, Democrats rallied against the measure because of the accompanying $1.5 billion in cuts to an Energy Department program that subsidizes low-interest loans to help car companies and parts manufacturers retool factories to build vehicles that will meet new, tougher fuel economy standards.
Democrats say cutting the loan program could cost up to 10,000 jobs because there wouldn't be enough money for all pending applications.
They estimated that $3.5 billion of loan subsidies has supported loans totaling $9.2 billion that created or saved 41,000 jobs in Tennessee, California, Indiana, Michigan, Delaware, Illinois, Kentucky, Missouri and Ohio. Ford Motor Co. and Nissan Motor Co.
have already received loans; Chrysler Group LLC is awaiting final approval of a loan.
Republicans countered that $4 billion remains in the loan fund, plenty to tackle the 11 loan applications closest to being approved. They also noted that Democrats didn't complain loudly when identical cuts sailed through the House when it passed the FEMA budget in June as part of a homeland security spending bill.
"The loan program ... has had excess funds for years," said House Appropriations Committee Chairman Harold Rogers, R-Ky. "All entities in final loan stages will still get the funding they've worked for."
For his part, Dicks said he was persuaded by fellow Democrats that fighting against the loan program cuts was worth the risk of taking down the must-pass stopgap measure.
"Our people feel very strongly about it. It has created jobs," Dicks said in an interview. "It's working, and so they want us to fight against (the cut)."