A bill that would remove the prosecution of military sexual assaults out of the chain of command faced defeat in the Senate on Thursday, falling just short of the 60-vote threshold needed to advance the legislation.

The Military Justice Improvement Act fell five votes short, with the Senate voting 55 to 45 to invoke cloture on the bill Thursday.

The measure was the brainchild of Sen. Kirsten Gillibrand, D-N.Y., who spent months lobbying senators to sign onto her bill. The legislation had the support of many groups representing survivors of rape and sexual assault in the military, but it was vehemently opposed by military brass. Gillibrand even drew the support of two unlikely allies - Sens. Ted Cruz, R-Texas, and Rand Paul, R-Ky.

"The people who do not trust the chain of command are the victims," Gillibrand said on the Senate floor Thursday before the vote. "That breach of trust, that fundamental breach of trust has been broken for victims of sexual assault."

The issue became a high-profile debate as it pit two Democratic women of the Senate against each other - Gillibrand and Sen. Claire McCaskill, D-Mo. McCaskill led the charge against Gillibrand's bill, arguing that stripping military commanders of their prosecution powers would undermine the military's authority.

Joining forces with Sens. Kelly Ayotte, R-N.H., and Deb Fischer, R-Neb., McCaskill introduced a bill of her own, which eliminates the "good soldier" defense and allows sexual assault victims to challenge the military if they are discharged from their service. Gillibrand has said she will support McCaskill's measure.

The vote came shortly after the Army suspended its top prosecutor for sexual assault cases after a lawyer who worked with him recently alleged he groped and attempted to kiss her at a sexual-assault legal conference more than two years ago.

Protect Our Defenders, a group representing survivors of military sexual assaults, expressed disappointment in the vote.

"It is a travesty that this very practical, conservative measure, supported by a substantial majority of the Senate and 60% of Americans was blocked by a procedural filibuster," Nancy Parrish, president of Protect Our Defenders. "We may have lost this battle due to political maneuverings, but effective reform will be accomplished. It is only a matter of time. We will redouble our efforts to secure the legal rights of American servicemen and women who have been sexually abused while serving their country."

Before Thursday's vote, McCaskill said she was disappointed that the disagreement between Gillibrand and McCaskill "overshadowed the amazing work that so many have done this year to enact a different day in the United States military."

Gillibrand countered, "This is not an opportunity to congratulate ourselves on the great reforms we've done."

Last year, the Senate approved historic reforms that were included as part of the National Defense Authorization Act of 2014. The reforms included stripping commanders of their ability to overturn jury convictions, providing independent counsel to each victim that reports a sexual assault, and requiring a dishonorable discharge or dismissal for anyone convicted of sexual assault.

The legislation also criminalized retaliation against victims who have reported a sexual assault, created a civilian review of cases that are not prosecuted and eliminated the statute of limitations on those cases.

Notably silent in the debate was President Obama, who has stressed the need to deal with sexual assaults in the military, but never weighed in on whether he would support Gillibrand's proposal.

Even if the Gillibrand bill would have passed the Senate, House Speaker John Boehner seemed unlikely to bring the measure to the House floor.

"The House and Senate have both acted on this issue and I frankly think that the agreement that was struck in the House in the Defense Authorization Bill strikes the correct balance," Boehner said today during a news conference at the Capitol. "And so I don't, frankly, see any reason at this point for any further action to be taken."

The Pentagon updated its sexual assault statistics Thursday, reporting a 60 percent increase in the number of sexual assault reports filed last year. There were about 5,400 reports in 2013 compared to 3,374 the previous year. Last May, a Pentagon survey estimated there were 26,000 instances of unwanted sexual contact, a 37 percent increase from the previous survey released two years prior.

ABC News' Luis Martinez and John Parkinson contributed to this report.