Top Border Patrol Official Resigned Amid Allegations of Improper Conduct

The supervisor then continued to plan the agent’s retirement party. Ms. Cali filed an employment discrimination complaint, but the ensuing investigation took nearly two years to complete.

“They hide sexual assaults and sexual harassment against mostly female agents,” said Jenn Budd, a former Border Patrol agent who left the agency in 2001 after she said she was sexually assaulted and beaten by a classmate at the Border Patrol training academy.

“The high-ranking male officers tend to get away with these crimes,” said Ms. Budd, who now speaks regularly to women in the agency who tell her they have been harassed by fellow agents.

Concerns about the culture at Customs and Border Protection were underscored last year when details about sexual harassment or misconduct at the Department of Homeland Security’s law enforcement agencies — including the Border Patrol — were found to have been withheld from an inspector general’s report, based on a draft released last year. The omission has fueled anxiety that there is little accountability for such behavior.

Since then, the Homeland Security secretary has reiterated his commitment to fair treatment in the workplace.

“It is our responsibility to provide every D.H.S. employee with a professional environment free of sexual harassment and other misconduct,” Alejandro N. Mayorkas wrote last year in an April memo addressing the missing inspector general findings.

People who have worked with Mr. Barker described him as widely respected.

Mr. Barker’s two-decade career at the Border Patrol was marked with one promotion after another. He was a key official involved in managing migration challenges at the southern border. During the Trump administration, he was detailed to the department’s front office to advise the secretary at the time, Kirstjen Nielsen.

Mr. Barker joined the Border Patrol in 2000 and served in posts in Houlton, Maine; Detroit; Sonoita, Ariz.; Del Rio, Texas; and Washington, D.C. He would have likely been a top contender to replace the current Border Patrol chief, Raul Ortiz, when Mr. Ortiz eventually retires.

Kitty Bennettand Seamus Hughes contributed research.