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WASHINGTON — Congress voted Thursday to keep the government financed through September, putting an end to a raucous first skirmish in this year’s showdown between Democrats and Republicans over federal spending while presaging bigger ones to come.

Scores of House Republicans deserted their leadership to vote against the bill, which cut $38 billion in spending, saying it did not go far enough. As a result, Speaker John A. Boehner was forced to rely on large numbers of Democrats to pass the measure, which subsequently sailed through the Senate, 81-19. It went to President Barack Obama for his signature.

Over the past several days, House Republican leaders repeatedly defended the bill, the product of a bipartisan compromise last week less than two hours before the government would have shut down. They said that while it fell short of their goal of cutting $61 billion from spending this year, it nonetheless established the principle that the budget would have to be substantially reined in.

The House vote was 260-167, with 59 Republicans breaking ranks to vote against the deal. The large number of defections highlighted the challenge facing Boehner as he tiptoes between conservatives who ran on a shake-it-up agenda and the limitations of what the House can do when Democrats control the Senate and the White House.

For all its last-minute drama and attendant partisan theatrics, the bill — made necessary after Democrats failed to pass a 2011 budget in the previous Congress — was just an opening act for more consequential battles to come before this Congress.

Thursday’s vote was the precursor to an expected vote Friday in the House on a budget blueprint for the next fiscal year that will call for a sea change in the structures of the Medicare and Medicaid entitlement programs, a measure almost certainly dead on arrival in the Democrat-controlled Senate. That fight, in turn, could be linked to the politically and economically explosive question of whether to approve an increase in the federal debt ceiling, a step many conservatives say they will resist unless Obama and his party agree to deep spending cuts for 2012 and beyond.

While opposing many aspects of the compromise budget bill for the remainder of this fiscal year, Democrats agreed to help lift it to passage. The minority leader, Rep. Nancy Pelosi of California, voted against the bill, while the Democratic whip, Rep. Steny Hoyer of Maryland, voted in favor.