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The Department of Veterans Affairsadministrator in charge of reducing the huge backlog of veterans benefits, who was a frequent target of critics, resigned on Friday despite a vast reduction in pending claims.

The administrator, Allison A. Hickey, became under secretary for benefits in 2011, overseeing 20,000 employees and benefits for more than 12 million veterans and their families. During her tenure, she emphasized a changeover from paper to digital claims, and the backlog in pending benefits claims declined from 611,000 in March 2013 to about 75,000 cases this week.

Veterans Affairs Secretary Robert A. McDonald praised her in a statement, calling her “an exceptional colleague and an even better friend,” and said he accepted the resignation with regret.

Ms. Hickey, a former Air Force brigadier general, had long been a contentious figure. The department’s own inspector general’s office questioned the reliability of reports of a shrinking backlog, and veterans groups had called for her removal. She was facing a new congressional inquiry this month into accusations that executives in her office used their positions to create plush jobs for themselves and bilk the government of thousands of dollars in moving expenses.

“She was not cut out for the job of V.A. under secretary for benefits,” Representative Jeff Miller, Republican of Florida and chairman of the House Committee on Veterans’ Affairs, said in a statement, adding that department statistics showing the backlog shrank on her watch “must be taken with a healthy grain of salt.”

Ms. Hickey was the department’s only top official left who had weatheredthe scandal of backlogs and wait times that caused the resignation of Secretary Eric K. Shinseki and the early retirement of the agency’s under secretary of health, Dr. Robert Petzel. Both left in 2014.

The American Legion, one of the largest veterans’ organizations, supported her resignation, saying in a statement, “Now that the three senior officials that were in place at V.A. have left office, the American Legion is optimistic that Secretary McDonald can finally make the cultural changes that he needs.”