The House's Democratic leaders, who had procrastinated for weeks over the bill, did not act in time to get the $33 billion to the troops by July 4 as the Pentagon had requested.
They added billions of dollars in non-military spending before passing the bill, so the measure must now return to the Senate. It passed the troop funds and its own set of disaster relief add-ons in May.
Both chambers must agree to the same legislation before it can go to Mr Obama for his signature into law. But the Senate is not in session again until July 12, and it is unclear how it will view the additions the House has made.
Pentagon chief Robert Gates said recently the money for 30,000 additional troops to Afghanistan should be approved by July 4 to avoid the Pentagon having to juggle accounts and possibly lay off civilians while continuing war operations.
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Still, it seemed a wonder the new money for the unpopular war got through the House at all, after long arguments among Democratic lawmakers over whether and how to do it. They set up a complicated series of votes in which the non-military spending passed 239-182, while the part that included the war funding passed 215-210.
"I do not believe this war is anything but a fool's errand. If I had my way, I would never bring this to the floor," declared House Appropriations Committee Chairman David Obey, who is in charge of spending legislation in the chamber.
The last two weeks have thrown an especially harsh light on the war effort, with new reports of corruption in President Hamid Karzai's government, and a change in the commander of US forces and multinational forces in Afghanistan.
The House-approved bill includes nearly $4 billion for the State Department to fund a civilian "surge," bringing economic aid to Afghanistan and its neighboor, Pakistan. The new money is in addition to about $130 billion Congress has already approved for Afghanistan and Iraq this year.