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WASHINGTON — House and Senate negotiators reached a final agreement Monday on a Pentagon policy bill that would strengthen protections for military victims of sexual assault and keep the prison facility at Guantánamo Bay open over President Barack Obama’s strenuous objections, as Congress rushed to wrap up work in its last full week of the year.

The way the Pentagon deal was struck reflected the dysfunction that has been characteristic of the current Congress. Negotiators from the House and Senate armed services committees found common ground on the sprawling measure even though a Senate version has yet to pass, and some Senate Republicans were furious that they had been bypassed once again.

But in the unusual first session of the 113th Congress, precedent has rarely held, and in a legislative year likely to go down in history as the least productive ever, Monday’s accord on defense policy was something of a victory for Congress.

It was a loss for champions of a more sweeping response to sexual assault in the military, a group led by Sen. Kirsten E. Gillibrand, D-N.Y. Her effort to take sexual assault cases out of the military chain of command was rebuffed and she intends to try to advance her bill again next year.

The House passed its annual defense policy bill in the summer, but the Senate’s version has been pending for weeks, bogged down in a dispute over the number of Republican amendments that would be allowed to come to a vote.

As Republican and Democratic leaders battled over procedure, the House and Senate armed services committees negotiated behind the scenes on a compromise bill that is likely to pass the House this week and then be taken up by the Senate next week.

The measure is the first change to laws governing sexual assault in the military in years and stems from the furor that has erupted in recent years over the rising number of sexual assaults in the military. There were 3,553 sexual assault complaints reported in the first three quarters of this fiscal year, a nearly 50 percent increase over the same period a year earlier.

The problem has drawn particular scrutiny in this Congress by the seven women on the Senate Armed Services Committee.

While the compromise measure offers modest reforms, the more contentious changes championed by Gillibrand were rejected by the Senate committee, seriously reducing the chances of her proposals being included in the final measure.

Sen. Carl Levin, D-Mich., who chairs the Senate Armed Services Committee, said the bill would provide a special victims counsel for survivors of sexual assault and makes retaliation for reporting assault a crime. Service members court-martialed for sexual assault would no longer be able to stay in the military if found guilty and those accused would be moved from units that they share with their accusers.