WASHINGTON – The Senate Armed Services Committee Wednesday rejected Sen. Kirsten E. Gillibrand’s effort to put prosecutors in charge of sexual assault cases in the military, as the panel’s chairman and other key senators voiced opposition to taking the prosecutorial power out of the chain of command.

A week after several top military leaders criticized Gillibrand’s proposal, Armed Services Committee Chairman Carl Levin said he favored replacing her proposal with one that increases independent review of sexual assault cases and criminalizes retaliation against victims, but that otherwise largely preserves the status quo.

“I do not support removing the authority of commanders to prosecute sexual assault cases and putting that decision in the hands of military lawyers outside of the chain of command,” Levin, D-Mich., said. “I believe that doing so would weaken our response to sexual assault and actually make it less likely that sexual assaults would be prosecuted.”

Gillibrand, D-N.Y., disagreed vehemently and vowed to try to get her amendment passed by the full Senate.

“I am deeply disappointed the voices of the victims of sexual assault have been drowned out by the military leaders who have failed to combat this crisis,” she said. “Our advocacy on this issue to remove the sole decision-making of the chain of command in serious crimes has only just begun.”

Only a day earlier, the Armed Services Personnel Committee, which Gillibrand chairs, had included her proposal in a bill that authorizes defense programs for fiscal 2014.

But now that bill will go to the Senate floor without the strongest Senate proposal to combat what Gillibrand and many other senators of both parties call an apparent epidemic of sexual assault cases in the armed services.

The legislation is not expected to reach the Senate floor until much later this year, and Gillibrand’s aides expect that she will be able to build support for her measure over time.

Wednesday’s committee vote suggests, though, that it could be an uphill battle that will by no means be fought along the Senate’s typical partisan lines.

The committee voted 17-9 to back Levin’s approach to the problem. Several key senators on military matters – including Republicans John McCain of Arizona, Lindsey Graham of South Carolina and Kelly Ayotte of New Hampshire – co-sponsored Levin’s approach, as did Democrats Claire McCaskill of Missouri and Jack Reed of Rhode Island.

Meanwhile, Gillibrand won the support of an unusual coalition of less-experienced senators, including Republicans David Vitter of Louisiana and Ted Cruz of Texas as well as Democrats Jeanne Shaheen of New Hampshire and Richard Blumenthal of Connecticut.

McCain and the other opponents of Gillibrand’s proposal praised her for her passion but said her proposal was a step too far that would erode the chain of command that’s the backbone structure of the American military.

“I think that when we give men and women the responsibilities of command, we should have them exercise those responsibilities,” McCain said.

McCain said the alternative that Levin had offered would be “extremely effective” by cracking down on retaliation and setting up a better review process for commanders’ prosecutorial decisions.

Gillibrand argued that a recent Pentagon study was all the evidence needed to push for a big change in how military sex crimes are prosecuted. The report showed that while the military believes 26,000 unwanted sexual contacts occurred in the military, only about 3,000 were formally reported.

“Victims tell us they do not report because of chain of command,” Gillibrand said.

Hearing that, Cruz decided to oppose Levin’s alternative, saying Gillibrand “made a powerful and effective argument that the lack of reporting is driven by a fear of not having an impartial third party outside the chain of command in which to report a sexual assault.”

While arguing in favor of giving trained military prosecutors rather than commanders the power to decide which cases to pursue, Gillibrand acknowledged that Levin’s alternative included some strong components, such as its criminalization of retaliation in such cases.

And supporters of Levin’s alternative stressed that their support was based on an honest disagreement about the best approach, not any desire to avoid the issue.

Senators are unanimous on one thing, McCaskill said.

“We are not going to give up our focus on this problem,” she said. Addressing the nation’s military leaders, she added: “We have just begun to hold your feet to the fire. We have just begun to hold you accountable.”