The future of the military justice system is uncertain this morning, as legislation aimed at stopping the growing number of sexual assaults in the armed forces was rejected by key members of Congress, on the grounds that the changes go too far. NBC's Kelly O'Donnell reports.

An effort to place military sex assault cases in the hands of an independent prosecutor was thwarted late Tuesday when Senate Armed Services Committee Chairman Carl Levin sided with the top brass – and against a fellow Democrat.

Levin (D-Mich.) will strip a proposal by Kirsten Gillibrand (D-NY) from the policy-setting Defense Authorization Act and replace it with a measure that instead requires senior military officers to review decisions when commanders refuse to prosecute a case.

Gillibrand’s proposal - which had 27 co-sponsors, including 4 Republicans – came in response to complaints that the U.S. military has repeatedly failed to deal with the issue of sex assaults. The military has resisted efforts to involve outsiders in its handling of such cases.

Aides for Gillibrand told NBC's Capital Hill correspondent Kelly O'Donnell that the move was "a real setback."

She is expected to make another attempt to introduce her proposal when the defense bill comes up for a final vote later this summer.

Levin, who is not seeking re-election, is expected to accept an amendment from Senator Claire McCaskill to prevent commanders from overturning jury verdicts.

The intra-party showdown is an example of the generational and gender divide on this issue - even as it has gained more attention and support with the additional women now in the senate.

Last month, a Pentagon report revealed that the number of service personnel who made an anonymous claim that they were sexually assaulted but never reported the attack skyrocketed from 19,000 in FY11 to 26,000 in FY12.

Embarrassingly, the report was published just a day after it was revealed that the Air Force's sexual-abuse prevention chief has himself been charged with sexual assault.

Last week, a female midshipman who accused three U.S. Naval Academy football players of raping her last year said her client was actually disciplined for drinking while her alleged attackers went unpunished.

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