WASHINGTON — Defense Secretary Lloyd Austin suggested to lawmakers Thursday that he supported changes to the way the military handles sexual assault cases, but he declined to endorse a measure long pushed by Sen. Kirsten Gillibrand, D-N.Y., that would cut the military chain of command out of the prosecution of many other serious crimes as well.

Austin’s support for changes around sexual assault cases represents a major shift for military leadership, which has long resisted calls to end the practice of handling such cases through the chain of command. But his opposition to broader changes to the military justice system proposed by Gillibrand could set up a showdown between a bipartisan group of senators and the Pentagon.

“Clearly, what we’ve been doing hasn’t been working,” Austin said in remarks before the Senate Armed Services Committee. “One assault is too many. The numbers of sexual assaults are still too high, and the confidence in our system is still too low.”

Rather than embrace Gillibrand’s bill, Austin appeared to endorse the recommendations of a panel he appointed to study the issue earlier this year. That panel recommended that independent military lawyers take over the role that commanders currently play in deciding whether to court-martial those accused of sexual assault, sexual harassment or domestic violence.

“The issues of sexual assault and sexual harassment,” Austin said, “are the problems we are trying to resolve and improve.”

President Joe Biden has signaled his support for Gillibrand’s broader approach, at least for now. Her bill has gained support from at least 70 members of the Senate — including many who voted against the same bill in 2014, arguing it would undermine commanders — and key members in the House.

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Sen. Jack Reed, D-R.I., chairperson of the Armed Services Committee, believes Gillibrand’s bill goes too far, and he has been working behind the scenes with Pentagon officials to rein it in.

“I want to be sure that whatever changes to the UCMJ that I recommend to the president and ultimately to this committee, that they are scoped to the problem we are trying to solve, have a clear way forward on implementation, and ultimately restore the confidence of the force in the system,” Austin said, referring to the Uniform Code of Military Justice, which is the foundation of the U.S. military legal system. “You have my commitment to that, and also my commitment to working expeditiously as you consider legislative proposals.”

Austin’s remarks could set off an intense political battle about which approach Congress will take. It will test the power of Gillibrand among her bipartisan Senate allies, including Sen. Chuck Schumer, D-N.Y., the majority leader, who could be forced to pick sides in determining the measure’s fate.

In either event, it seems clear that commanders are all but certain to lose full control over sexual assault prosecutions. “Change is coming to the department,” Reed said.

Gillibrand and one of her Republican colleagues on the committee, Sen. Joni Ernst of Iowa, further pressed Austin on his views of the issue during the hearing. Gillibrand suggested that failure to include other serious crimes in the legislation would contribute to racial disparities in court-martial cases, which seemed to be part of a strategy to appeal to the remaining skeptical members of Congress and Austin.

But while Austin took pains to praise Gillibrand’s work on the matter over the past decade, he also signaled that he did not support the broad nature of her legislation.

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“Whatever changes occur going forward will be largely due to your incredible dedication to this issue,” he told Gillibrand. “As you know, Senator, I always have an open mind to solving any tough problem,” he said, adding that his commission had been focused on sexual assault and harassment.

When he was confirmed by the Senate, Austin said that dealing more forcefully with sexual assault would be a top priority. In February, he appointed the independent commission to examine the issue and give recommendations that he and the service chiefs could consider.

The members of the panel are seeking to create a new career track in the Defense Department in which judge advocates general — military lawyers — would be specially trained to deal with such cases. This alone would be a major shift in how the military does things. Austin has said he wants the service chiefs to review the recommendations.

Kathleen Hicks, the deputy defense secretary and the first woman to serve in the No. 2 role at the Pentagon, and Gen. Mark Milley, chair of the Joint Chiefs of Staff, have both said they have become convinced that the current system does not serve victims well.

“I have some evidence, some studies, some anecdotal evidence that junior members of the military, primarily women, have lost faith and confidence in our chain of command to resolve sexual assault through the chain of command,” Milley said Thursday.

But bringing in other felonies to any overhaul of the military justice system, he said, “requires some detailed study,” adding that he had “a complete open mind on this.”

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A report out of Fort Hood, Texas, last year that detailed a culture of harassment and abuse gave fuel to Gillibrand’s measure and parallel efforts in the House.

In 2019, the Defense Department found that there were 7,825 reports of sexual assault involving service members as victims, a 3% increase from 2018. The conviction rate for cases was unchanged from 2018 to 2019; 7% of cases that the command took action on resulted in conviction, the lowest rate since the department began reporting sexual assault cases in 2010.

Leaving the hearing, Gillibrand seemed undeterred in her push for her legislation.

“This is something that the majority of the committee has already formed a view on,” she told reporters. “There are so few pieces of legislation in Congress today that both Liz Warren and Ted Cruz support, one that both Chuck Schumer and Mitch McConnell support. This is widely bipartisan, has the majority of the committee, and this is not a new issue.”