WASHINGTON – The U.S. Senate overwhelmingly approved a bill late Monday making big changes in the military justice system to deal with sexual assault, including scrapping the nearly century-old practice of using a “good soldier defence” to raise doubts that a crime has been committed.

On a vote of 97-0, the Senate rallied behind a bipartisan plan crafted by three female senators — Democrat Claire McCaskill and Republicans Kelly Ayotte and Deb Fischer— that would impose a half-dozen changes to combat the pervasive problem of rape and sexual offences that Pentagon leaders have likened to a cancer within the ranks.

“Unanimous agreement in the U.S. Senate is pretty rare — but rarer still is the kind of sweeping, historic change we’ve achieved over the past year in the military justice system,” McCaskill said after the vote.

Still, that unanimous support was in sharp contrast to last week, when military leaders vigorously opposed a measure by Sen. Kirsten Gillibrand that would have stripped commanders of their authority to prosecute cases and given that power to seasoned military lawyers outside the chain of command. The Senate voted 55-45 for that farther-reaching bill, but that was five votes short of the necessary 60.

Though expressing certain reservations, the Pentagon had been generally accepting of the new bill.

The House could act on the legislation as a stand-alone measure or incorporate it into the massive defence policy bill that it pulls together in the spring.

This “is not the end of this,” Ayotte said in brief remarks on the Senate floor after the vote. “We will make sure reforms are implemented, commanders are held accountable and victims are treated with dignity and respect.”

The new legislation would change the military rules of evidence to prohibit the accused from using good military character as an element of his defence in court-martial proceedings unless it was directly relevant to the alleged crime. The “good soldier defence” could encompass a defendant’s military record of reliability, dependability, professionalism and reputation as an individual who could be counted on in war and peacetime.

McCaskill described it as “the ridiculous notion that how well one flies a plane should have anything to do with whether they committed a crime.”

Under the bill, the defence could still be used in the sentencing phase. The Pentagon has indicated that it is crucial as commanders adjust sentences to allow for plea agreements.

The measure also would give accusers a greater say in whether their cases are litigated in the military system or civilian and would establish a confidential process to allow alleged victims to challenge their separation or discharge from the military. In addition, it would increase the accountability of commanders and extend all changes related to sexual assault cases to the service academies.

The Pentagon has estimated that as many as 26,000 military members may have been sexually assaulted in 2012, based on an anonymous survey. Many victims are still unwilling to come forward despite new oversight and assistance programs aimed at curbing abuse, the military says.

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Associated Press writer Lolita C. Baldor contributed to this report.