In her letter to Morton, Barr said she has been the subject of "unfounded allegations designed to destroy my reputation" and is resigning "with great regret."
"Of greater concern however, is the threat these allegations represent to the reputation of this agency and the men and women who proudly serve their country by advancing ICE's mission," Barr wrote. "As such, I feel it is incumbent upon me to take every step necessary to prevent further harm to the agency and to prevent this from further distracting from our critical work."
Barr went on leave last month after the New York Post reported on the lawsuit filed by James T. Hayes Jr., ICE's special agent in charge in New York. Additional employees came forward with their allegations around the same time.
House Homeland Security Committee Chairman Peter King, R-N.Y., said in a statement Saturday that Barr's resignation "raises the most serious questions about management practices and personnel policies at the Department of Homeland Security." He said his committee will continue to review the case and personnel practices at DHS.
In one complaint, Barr is accused of telling a male subordinate he was "sexy" and asking a personal question about his anatomy during an office party. In a separate complaint, she is accused of offering to perform a sex act with a male subordinate during a business trip in Bogota, Colombia. She's also accused of calling a male subordinate from her hotel room and offering to perform a sex act. The names of two of Barr's accusers were censored in affidavits reviewed by AP.
Homeland Security's office of professional responsibility and inspector general have been investigating the allegations.
Prior to the lawsuit, there were no complaints about Barr, according to a homeland security official who spoke to the AP on condition of anonymity because he was not authorized to speak publicly about the matter.
In the lawsuit, Hayes described a "frat house" atmosphere at ICE designed to humiliate male employees under Barr's leadership. Hayes, who was transferred to New York from ICE headquarters in Washington, is asking for more than $4 million that, among other things, would cover compensation he believes he is owed for relocation expenses and financial losses associated with his transfer.
Hayes' lawyer, Morris Fischer of Silver Spring, Md., has declined to comment.
The Justice Department is seeking to dismiss Hayes' lawsuit on the basis that he did not state a claim for retaliation.
Barr, a 1995 graduate of the University of Arizona, was among Napolitano's first appointments after she became secretary in 2009. Barr started working for Napolitano in 2004, while Napolitano was governor of Arizona. Prior to that, Barr worked for Arizona Republican Sens. Jon Kyl and John McCain.