The Senate rejected a proposal Thursday that would dramatically overhaul how the Defense Department handles assault and rape cases involving military personnel, voting down a proposal that would remove military commanders from the decision about whether these cases should be prosecuted.

Congress has already voted to revamp the military’s legal system by ending the statute of limitations on assault and rape cases and making it a crime to retaliate against victims who report assaults. It also voted to require dishonorable discharge or dismissal of anyone convicted of sexual assault or rape.

But on Thursday, senators rejected a plan by Sen. Kirsten Gillibrand (D-N.Y.) that would go further by taking away from military commanders the power to refer serious crimes to courts-martial. If enacted, that decision would have shifted to professional military trial lawyers operating outside the chain of command.

The proposal fell five votes short of the 60 votes necessary to clear a procedural hurdle and proceed to a final consideration. Ten Democrats voted against Gillibrand’s plan, while 11 Republicans, including Senate Minority Leader Mitch McConnell (Ky.), joined her in voting to advance the bill.

After the vote, Gillibrand said that the changes enacted by Congress “have not gone far enough. We know that the deck is stacked against victims of sexual assault in the military today — and today, sadly, we saw the same in the halls of Congress.”

Paul Rieckhoff, founder of Iraq and Afghanistan Veterans of America, a group that backed the proposal, said its rejection was “a missed opportunity” for senators to further address concerns about sexual violence in the ranks. “They have turned their back on veterans and servicemembers who pushed for reform,” he said in a statement.

A separate, more modest proposal by Sen. Claire McCaskill (D-Mo.) cleared a Senate procedural vote Thursday and is expected to be approved Monday night.

The votes came only hours after the Army said it is investigating its top sex-crimes prosecutor on allegations that he groped a female lawyer at a sexual-assault conference in 2011.

Lt. Col. Joseph Morse, who supervises 23 other special-victims prosecutors for the Army, has not been charged in the case but was recently placed under criminal investigation after the female lawyer reported the alleged 2011 incident, officials said.

News of the case was first reported Thursday by Stars and Stripes, a newspaper that covers military affairs.

The Army declined to comment publicly on the report. But two Army officials, speaking on the condition of anonymity because the investigation has not been completed, confirmed that Morse was under investigation after a female lawyer who once worked for him reported that he groped her in a hotel room during a sexual-assault conference in Alexandria.

Morse is chief of the Army’s trial counsel assistant program, which is based at Fort Belvoir, and trains prosecutors throughout the Army. He also oversees nearly two dozen special-victim prosecutors who focus on sex crimes, domestic violence and crimes against children. He did not return a phone call Thursday to his Fort Belvoir office seeking comment.

The revelation is just the latest blow to the Pentagon as it struggles to cope with what some leaders have acknowledged is an epidemic of sexual assaults in the ranks. In response, Congress voted last year to dramatically overhaul the military’s legal system by ending the statute of limitations on cases of sexual assault or rape and stripping military commanders of the ability to overturn jury convictions in sexual assault and rape cases, among dozens of other reforms.

Gillibrand chairs a Senate Armed Services subcommittee on military personnel and led the charge for bolder changes by aggressively lobbying skeptical colleagues and sparring in open hearings with Pentagon leaders who oppose her proposal.

Despite the setback, supporters said Thursday that they will continue pushing for changes.

“We will not be stopped,” Sen. Barbara Boxer (D-Calif.) told reporters. “Look, I’ve been here long enough to see how sometimes change is painful and slow. But it happens. I’ve seen it. And we will see it again.”

At the other end of Capitol Hill Thursday, Rep. Jackie Speier (D-Calif.), a supporter of Gillibrand’s proposal, questioned Gen. Martin Dempsey, chairman of the Joint Chiefs of Staff, over the military’s handling of another embarrassing episode involving raunchy and sexist e-mails written by an Army commander.

The commander, Brig. Gen. Martin Schweitzer, sent e-mails to two other Army officers in 2011 in which he called Rep. Renee L. Ellmers (R-N.C.) “smoking hot” and joked how he had masturbated “3 times over the past 2 hours” after meeting with the congresswoman. Schweitzer was later rebuked by the Army, and his selection to be promoted to the rank of major general was placed on hold. The existence of the e-mails was first reported by The Washington Post in January.

During a hearing of the House Armed Services Committee, Speier asked Dempsey why the Army had not taken tougher action against Schweitzer. He is currently assigned to the Joint Staff and serves under Dempsey.

“I question what the punishment is when this general is now working for you, General Dempsey,” Speier said.

Dempsey replied that he couldn’t talk about the case because it “is part of an ongoing investigation.”