The opposition from the Parliament, which was given the formal power to veto budgets under the Lisbon Treaty of 2009, presents a significant hurdle. As a result of the vote Wednesday, the governments of the Union’s 27 member states must now work out another compromise — this time with Parliament. The process could take months.

“It was foreseeable that the European Parliament would refuse,” Martin Schulz, the president of the legislature, said at a news conference shortly after the vote. “We don’t want to see the European Union going in the direction of a deficit union.”

Mr. Schulz was referring to resistance by some national governments to allocating more money at the start of each year to ensure that projects are fully funded from 2014 to 2020, the period of the budget.

The Parliament’s resolution called on E.U. governments to settle their outstanding bills and to give scope to the Parliament and to E.U. governments to move funds among different areas of the budget to meet needs as they arise. That means money that might ordinarily go unspent would be spent, but without changing the overall budget figure.

But the resolution also called for a review of the budget with the possibility of increasing spending. Many members of Parliament said that raising the overall amount of the budget should be an option, particularly if the economic crisis now gripping the Union tapered off. The decision about who would conduct the review is likely to be an important part of the negotiations in coming months.