Acting defense secretary Patrick Shanahan said the survey makes clear that the Pentagon must do more to address the culture that allows sexual assaults and harassment to persist.

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“To put it bluntly, we are not performing to the standards and expectations we have for ourselves or each other,” he said in a memo. “This is unacceptable. We cannot shrink from facing the challenge head on. We must, and will, do better.”

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The elevated numbers add fuel to a contentious debate about sexual misconduct in the military and the role commanders play in determining whether to initiate legal proceedings. That role is defended by many service members who see it as critical to command structure and condemned by critics who charge it is a holdover from an earlier era and fosters bias.

Those conflicting views — brought to public attention after the 1991 Tailhook scandal exposed the prevalence of sexual misconduct — were reignited this year when Sen. Martha McSally (R-Ariz.), a retired fighter pilot, revealed during a Senate hearing that she had been raped while in the military.

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McSally, who did not immediately report the attack, told a riveted audience that when she did decide to talk about it, she felt as if “the system was raping me all over again.” She then sided with tradition, arguing that “the commander must not be removed from the decision-making responsibility of preventing, detecting and prosecuting military sexual assault.”

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For those who argue that independent military prosecutors, and not commanders, should decide whether to pursue these cases, McSally’s testimony dashed hopes as quickly as it raised them.

“It was a step forward and a step back,” said Don Christensen, who is president of the victims advocacy group Protect Our Defenders and was in the hearing room — a step forward for a leader of McSally’s stature to share her horrific experiences but a setback, he said, to hear her conclusion.

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McSally was the first American woman to fly in combat and the first female commander of a fighter squadron. She also successfully sued the secretary of defense in 2001 over a requirement that women serving in Saudi Arabia cover themselves in abayas whenever they traveled off base.

McSally, who later said she came forward “to give some hope” to other survivors, declined to be interviewed for this article. In a statement issued Thursday, she said sexual assault “whether in the military or in communities across our country is abhorrent and intolerable.”

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“The numbers released today confirm that the time is now to impart lasting change within the military and that it is more urgent than ever,” she said.

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During the Senate hearing, she criticized commanders who do not want the responsibility, saying they have a duty to “stay at the center of the solution.”

Retired Marine Sarah Plummer Taylor, who said she was raped early in her military career, derived no hope from McSally’s testimony. “I don’t know how you could have lived that and then say [the system] should stay,” she said. “I am not a lawyer, but for the most part we should be aiming for impartiality, at least for a neutral start.”

Many proponents of change speak about how their exposure to the civilian system influenced them — and how the ongoing debate in Congress reflects a loss of civilian power over the military. A potent combination of history and culture, they say, underlies fidelity to the current way of doing things.

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Passed by Congress in 1950, the Uniform Code of Military Justice, based in 18th-century command structure, is the foundation for the military’s parallel legal system. It applies to all U.S. military members worldwide and governs all offenses, from straggling to spying to mutiny and murder, whether or not the crimes are related to service. Service members can be recalled to active duty to face charges under the code, even after they retire.

“If Senator McSally robbed a bank, she could be prosecuted in a court-martial,” said Eugene R. Fidell, a specialist in military law who is one of the attorneys challenging the constitutionality of court-martial jurisdiction over retirees in a current case in U.S. District Court, Larabee v. Spencer.

Other countries, including Britain, Canada and New Zealand, have adopted independent prosecutors — a practice championed by Sen. Kirsten Gillibrand (D-N.Y.), who has led the charge in Congress to get the United States to follow suit through the Military Justice Improvement Act, aimed at professionalizing the prosecution of serious crimes.

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“The status quo is not working,” Gillibrand said in a statement. “It’s time for Congress to step up and bring accountability where the Department of Defense has repeatedly failed.”

Commanders may be motivated by concerns such as avoiding high court-martial numbers, which could reflect problems in their leadership, or perhaps protecting a phenomenal fighter pilot, said Christensen, who was a prosecutor, defense counsel and military judge during his career in the Air Force.

“It’s easy to prosecute people you don’t like,” he said, “and hard to prosecute people you like.”

'Defendant friendly'

During 20 years as a lawyer and judge in the Air Force, Joshua Kastenberg oversaw numerous cases involving sexual violence. But it was only after he had left the service and studied other countries’ military legal systems that he became convinced that Congress should take that model seriously.

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Kastenberg, now a law professor at the University of New Mexico, still looks back on a case involving an airman, Brandon Wright, who was accused of aggravated sexual assault. Wright was acquitted in 2015 after two investigations over three years, first in Europe, where the alleged assault took place, and then in Washington.

Kastenberg believes the case was moved to Washington in part for political reasons. In a ruling at the time, he described commanders’ concerns that “the failure to have charges preferred against SrA Wright would enable Senator Kirsten Gillibrand to gain needed votes on a pending bill to remove commanders from the court-martial process.”

“A prosecutor bound by rules of ethics would think long and hard before knowingly taking part in that process,” Kastenberg said.

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Ryan Guilds, a civilian lawyer at Arnold & Porter and the woman’s independent counsel in the case, subsequently published an open letter to survivors, describing the protracted and invasive experience and warning that “the military justice system is defendant friendly.”

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Not every former military judge agrees that commanders should be replaced in all cases.

“I don’t trust lawyers any more than I trust commanders,” said Rachel VanLandingham, former judge advocate in the Air Force. “Why would we want to ignore their vast experience?”

But VanLandingham said her views evolved after she left the military and started teaching criminal law at Southwestern Law School “and gaining more objectivity.”

She said Gillibrand’s bill goes too far, arguing that overall responsibility for criminal justice should remain commander-focused, but she puts sexual assault into a different category.

“There is something different in these crimes — and a very strong argument that you can and should treat these differently,” she said.

'They have final say'

It was a desire “to gain outside attention to the epidemic of rape and sexual assault in our ranks” that led Coast Guard veteran Kori Cioca to file a class-action suit in federal court for compensation against former defense secretary Robert Gates and his predecessor, Donald H. Rumsfeld.

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The case, which was featured in the 2012 documentary “The Invisible War,” was dismissed. But Susan Burke, the Baltimore-based lawyer who represented Cioca and a group of other survivors, gained insights into the common core of their stories.

“It all leads back to the command, because they have final say in everything, ” Burke said.

Changing the legal process is only a first step, said Leigh Goodmark, a professor of law at the University of Maryland who said the military as a microcosm of a broader challenge of shifting cultural norms.