The confirmation of President Trump’s pick to become the U.S. military’s No. 2 officer could be delayed as senators question how the Pentagon handled sexual assault allegations against him, even though military authorities deemed them insufficient to bring charges.

Trump nominated Air Force Gen. John E. Hyten, commander of U.S. Strategic Command, to become the next vice chairman of the Joint Chiefs of Staff in early April.

Shortly thereafter, an Army colonel who had been relieved of her duties while serving on his staff for allegedly creating a toxic work environment alleged that Hyten had made sexually abusive contact with her on more than a half dozen occasions, including in a California hotel room during the Reagan National Defense Forum in December 2017. 

The allegations — which Hyten denies — prompted a probe by the Air Force criminal investigative service. Based on the results, the Air Force decided not to press forward with a court-martial or any other disciplinary actions against Hyten, who is in charge of the nation’s nuclear arsenal. 

“After a comprehensive investigation by the Air Force Office of Special Investigations, there was insufficient evidence to support any finding of misconduct on the part of Gen. Hyten,” Pentagon spokeswoman Col. DeDe Halfhill said in a statement. “With more than 38 years of service to our nation, Gen. Hyten has proven himself to be a principled and dedicated patriot.”

Air Force officials briefed senators on Wednesday morning about the results of the investigation.

A senior U.S. military official said investigators spoke to 53 people in three countries and 13 states, reviewed thousands of emails, and ended up “out of rocks to turn over” after following all the leads provided. After interviewing people who previously served under Hyten, investigators didn’t find indications of such behavior with other subordinates, said the military official, who like others spoke on the condition of anonymity to discuss the details of a legal matter.

“Did we find a case where the service member says on this date, x happened, and when we looked at it, they were on different continents? We didn’t,” the official said. “So was it physically possible? Yes.” 

The Army colonel who made the allegations said she is willing to testify under oath to the Senate Armed Services Committee, which is overseeing Hyten’s confirmation process, preferably in a closed-door session. Speaking to The Washington Post, she described the military justice system that adjudicated her case as flawed and said the alleged incidents merit action by the military as Hyten prepares to ascend to a position of even greater power.

The Army colonel, who said she was in the force for 28 years, including two tours in Afghanistan and two tours in Iraq, and had served a variety of prestigious assignments involving high-level strategy, said she didn’t tell anyone about the incidents at the time.

A spokesman for Hyten at Strategic Command declined to make the general available for comment. In a statement, the spokesman said Strategic Command fully cooperated with the investigation.

Members of the Senate Armed Services Committee have already questioned the Pentagon about its handling of the case. In a June 25 letter to acting defense secretary Mark Esper, Sen. Elizabeth Warren (D-Mass.) and Sen. Tammy Duckworth (D-Ill.) said they had “serious concerns and questions” about the procedures the Department of Defense followed during the investigation.

The senators said they were “gravely troubled” that the Pentagon designated an Air Force general who was junior in grade to Hyten to decide whether to proceed to a court-martial or other disciplinary measures. Gen. James M. Holmes, commander of Air Combat Command, who is part of a small Air Force four-star general officer corps along with Hyten, served as the convening authority in the case.

Warren and Duckworth also expressed concern that Hyten wasn’t removed or suspended from his post at U.S. Strategic Command during a criminal investigation against him and retained his security clearance during the process.

“That he remains in command while under criminal investigation raises serious questions about whether the Department is affording General Hyten preferential treatment because of his rank and pending nomination,” the senators wrote.

The senior U.S. military official said the department decided to make Holmes the convening authority for the case to leave room for the possibility of appeal to the defense secretary or the secretary of the Air Force. The official said Holmes had “zero conflict of interest” because he didn’t work for Hyten, wasn’t from the same community of nuclear and space officers, and wouldn’t work for him in the future.

An Air Force official said no evidence was produced that was sufficient to warrant the revocation of Hyten’s security clearance or temporary removal from his position. 

The Army colonel said she contacted senators to raise concerns that the matter wasn’t going to be handled fairly because one of Hyten’s fellow four-star Air Force generals was adjudicating the case.

The situation risks imperiling the confirmation of one of the nation’s top military officials at a time of unprecedented leadership upheaval at the Pentagon. The Department of Defense is set to be led by its third acting defense secretary this year, as Esper prepares to comply with federal rules by stepping aside temporarily while his nomination is considered.

There is also uncertainty in the uniformed ranks. The four-star admiral who was due to take over as the Navy’s top officer on Aug. 1 instead abruptly announced his retirement last weekend, citing his interactions with a subordinate accused of acting inappropriately toward female officers. Gen. Paul J. Selva, the current vice chairman of the Joint Chiefs of Staff, is due to retire on July 31.  

Whether the situation will prevent Hyten from assuming the military’s No. 2 post may turn on whether senators believe the word of an Army colonel over that of a four-star Air Force general — and whether the White House, the Pentagon and Hyten himself decide to proceed with the process.

The Army colonel, who spoke on the condition that The Washington Post not use her name but agreed to be described by her service and rank, characterized a series of incidents in which she alleged Hyten touched, hugged or kissed her without her consent, and spoke of his feelings for her. In many of the alleged incidents, she said she rebuffed him or warned him that his actions were inappropriate. 

The colonel said the first incident occurred during a visit to Palo Alto, Calif., in January 2017. She had stayed behind in Hyten’s hotel room after a team meeting, she said, and the general pressed her hand to his groin as she tried to leave. She said she did not report that incident, wondering if it had been a mistake.

Other alleged incidents followed, she said, culminating in one during another trip to California, this time for the Reagan National Defense Forum outside of Los Angeles in December 2017. The colonel said Hyten appeared at the door of her hotel room in his workout clothes. Once inside, she said that he began kissing her aggressively and grinding against her body until he ejaculated. 

“I felt really violated and really disappointed,” she said.

She said she didn’t tell anyone about what had happened until much later because she thought she could manage the situation and she believed that because Hyten planned to retire after his Strategic Command assignment, there would be no further chance of other subordinates facing similar conduct. 

During all that time, the colonel said, Hyten praised her and advocated for her career, recommending her to other senior officers as she sought a position outside of Strategic Command. That changed early in 2018, she said, when Hyten’s command opened a formal investigation into allegations that she had helped create a hostile environment. 

A different officer who was on Hyten’s team said the Army colonel was short-tempered, responded angrily to not getting her way, and yelled at other officials, even though she sometimes was a well-versed leader able to connect the dots between Strategic Command and Washington.

The Army colonel denied yelling and said she was under stress because of the alleged inappropriate behavior by Hyten. “In hindsight, I could have been much more levelheaded,” she said. “I could have. But to sit here and say I was a toxic leader is not true.”

In March 2018, Hyten signed off on a decision to relieve her of her duties. Later that year, she assumed a senior role at a different command and is expecting to retire as a colonel. 

The other officer formerly on Hyten’s team, who lacked authorization to speak publicly, suggested that the Army colonel also raised allegations of a nonsexual nature against Hyten that weren’t substantiated. The colonel confirmed that as part of her appeal against the inquiry that lead to her dismissal, she had pointed out what she described as Hyten’s questionable travel and ethics issues. She said she provided statements to an inspector general investigation regarding those matters but didn’t know the outcome. The Post was not able to verify what resulted from those allegations.

The colonel denied that she had leveled any allegations as retribution for being relieved of her duties.

“I was ready to go to my grave with this because I didn’t want to have to deal with it,” she said. That changed when Hyten emerged as the president’s choice to replace Selva, she noted. 

“I saw that nomination come out and I freaked out,” she said. 

“I was like I won’t be able to live with myself if I don’t and this happens to somebody else,” she added. “So that was a no-brainer for me.”

Hyten hasn’t spoken publicly about the matter. Pentagon officials didn’t immediately respond to a request for comment on the specifics of the allegations.

Members of the Senate Armed Services Committee are now combing through the details of the case.

“Anytime there are allegations, it’s a concern,” Sen. Mazie Hirono (D-Hawaii) said, exiting a meeting of senators on the panel, in which they were told of the findings of the investigation.

Sen. Jack Reed (R.I.), the ranking Democrat on the panel, declined to say whether he intended to insist on hearing from the Army colonel. 

“We are taking this step by step. The first step is getting the appropriate briefings from the investigations,” Reed said as he exited the same meeting. 

Duckworth said Wednesday that committee members had not been given the full investigative report but were promised an unredacted copy.

Emerging from the meeting with Pentagon officials about the Hyten investigation, Duckworth said she continued to be concerned that Hyten “wasn’t removed from his position, or suspended from his position, when that has happened with previous high-ranking members of the military” facing similar charges.

Duckworth, who is an Army veteran, said she thought it would be important to hear from the Army colonel , though she said how hard Democrats would push for that would be left up to Reed.

But, Duckworth noted, “She’s been in touch with my office, and she’s been in touch with quite a few of our offices already.”

Sen. Martha McSally (R-Ariz.), a veteran of the Air Force who was sexually assaulted while serving, noted she had “a lot more questions” and was working through the materials officials had provided to the panel.

“I’m doing my due diligence,” she said, “like we should with everybody.”

Julie Tate contributed to this report.