The Pentagon and the surrounding area is seen in this aerial view in Washington on Jan. 26, 2020. Pablo Martinez Monsivais/Associated Press file

President-elect Donald Trump’s Pentagon pick Pete Hegseth, who has denied allegations that he sexually assaulted a woman in 2017, would lead an agency that has long faced criticism over its handling of sexual assault and harassment allegations.

As defense secretary, Hegseth would oversee around 3 million military and civilian personnel and a recently reformed process for prosecuting sexual assault and other serious crimes.

Advocates for survivors of sexual assault in the military have warned that placing a man accused of assault in charge of the Pentagon could have a chilling effect on reporting of sexual misconduct.

The allegations could “silence women and men who are sexually assaulted from coming forward,” said Don Christensen, a retired colonel who was chief prosecutor for the Air Force. “There’s a lot of bureaucratic barriers, there’s a lot of isolation, social retaliation, professional retaliation against victims,” Christensen said. “Then you put at the top of the Department of Defense someone who is accused of doing what they are accusing their perpetrator of doing, it’s just not going to be something that builds confidence.”

Hegseth has also faced scrutiny over allegations that he often drank to excess. In an interview with Megyn Kelly, Hegseth said he “never had a drinking problem.” The New Yorker recently reported that he was forced to leave two nonprofit groups he led amid “serious allegations of financial mismanagement, sexual impropriety, and personal misconduct.” Hegseth’s attorney dismissed that story, describing its content as “outlandish.”

But the assault allegation, which led to a nondisclosure agreement between Hegseth and the alleged victim, but no criminal charges, has been central to critics’ worries about Hegseth. And as Hegseth prepares for a confrontational Senate confirmation process, he is all but guaranteed to face questions about how the Pentagon would handle assault cases under his leadership.

Pete Hegseth, President-elect Donald Trump’s nominee to be defense secretary, is joined by his wife Jennifer Rauchet, as they walk through the basement of the Capitol on Wednesday in Washington. Mark Schiefelbein/Associated Press

One of the key senators Hegseth will need to win over is Sen. Joni Ernst, R-Iowa, a military veteran and survivor of sexual assault whom he met with on Wednesday. In a post on X, Ernst said she and Hegseth had a “frank and thorough conversation.”

In a statement to The Washington Post, Hegseth said that if confirmed, he would “ensure the military has zero tolerance for sexual assault or harassment so that women continue to feel welcome to serve.”

“I will work diligently, including with fellow leaders on this topic in the Senate, to continue to fix what’s broken to prevent sexual assault in the first place, but when it tragically does occur, women feel safe to report, the justice process is clear and fair, and the entire Department adheres to the Uniform Code of Military Justice,” Hegseth added.

The U.S. military has long struggled to address sexual assault, which lawmakers have described as an epidemic that affects thousands of service members each year. In 2021, Ernst worked with Sen. Kirsten Gillibrand, D-New York, on legislation to overhaul the system for handling military sexual assault cases. That year, Congress passed legislation setting up a two-year process to strip the military chain of command of its responsibility for sexual assault prosecutions, a decision that military leaders had long resisted but advocates for survivors had long sought.

Advocates for survivors are unconvinced that Hegseth is the right choice to oversee the new process, which relies on Offices of Special Trial Counsel within the Pentagon to handle prosecutions of service members accused of sexual assault and other serious crimes.

Kayla Williams, who served on an independent review commission that investigated sexual assault in the military and was assistant secretary of public and intergovernmental affairs at the Department of Veterans Affairs under the Biden administration, also expressed concern about a chilling effect on the willingness of survivors to come forward if Hegseth is confirmed.

“When I think about my own experience just on a very personal level, when I saw that minor infractions had been ignored by my leadership in the military once there were more severe infractions, I absolutely did not even consider reporting them,” Williams said “Why go through the embarrassment and pain and hassle? As a woman, if you report sexual assault or harassment in the military, you are treated badly. So why expose yourself to that if you think nothing is going to be done?”

Hegseth’s “documented opposition to inclusion, history of misconduct allegations, and willingness to reverse progress on critical reforms disqualify him for this role,” Nancy Parrish, founder and CEO of the nonprofit Protect Our Defenders, said in a statement released last week.

A new defense secretary might find it difficult to unwind legislative changes to the military’s system for reporting sexual assault claims, Williams and other experts said. However, a defense secretary could affect who leads the Offices of the Special Trial Counsel and could influence the types of cases they prosecute.

Trump has not indicated whether he would seek to reverse the recent changes.

As a candidate in 2016, Trump opposed removing sexual assault prosecutions from the military chain of command. Trump acknowledged at an NBC forum in September of that year that sexual assault in the military was a “massive problem” but said that he wanted “to keep the court system within the military.”

“The numbers are staggering, hard to believe, even – but we’re going to have to run it very tight. I, at the same time, want to keep the court system within the military,” he said. “I don’t think it should be outside of the military.”

Trump’s position on the issue was not controversial within the military, said Rachel VanLandingham, a former Air Force attorney who is a professor at Southwestern Law School.

“I don’t feel like it was a Trump administration failure to oppose removing prosecutorial discretion from commanders for sexual assault and other crimes, that was the standing line of every single military officer,” VanLandingham said. “I think the Trump administration made strides in dealing with recognizing the importance of reducing sexual assault in the ranks and I think they did make improvements in that arena.”

During his first term, Trump met with the family of Spec. Vanessa Guillén, a 20-year-old, whose remains were found after she disappeared from Fort Hood, a Texas post since renamed Fort Cavazos, in 2020. Before her disappearance, Guillén told her family that she had been sexually harassed but worried about telling her leaders, according to her family. In response to Guillén’s death, Army Secretary Ryan McCarthy ordered an independent civil review of Fort Hood, which found a “permissive environment for sexual assault and harassment.” However, the military chain of command remained in charge of sexual assault prosecutions until after Trump left office.

Hegseth, a former Fox News host, has also drawn scrutiny for his advocacy for U.S. service members accused of war crimes. His advocacy helped lead to Trump’s pardons for two Army officers in separate murder cases. He has also criticized the Obama administration’s decision to allow women to serve in direct combat roles, suggesting that doing so “has made fighting more complicated.”

VanLandingham said that she is more worried about how Hegseth would approach war crimes than how he would handle sexual assault cases, observing that “President Trump has shown himself to follow the lead of Mr. Hegseth and to shut off accountability for those that deserve it.” But the vast new infrastructure to investigate and prosecute sexual assault allegations will be hard to dismantle, she said.