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Ranking Democrat Rep. Elijah E. Cummings of Maryland said all sides must work to prevent a recurrence.

Ms. McCarthy’s role, though, remains particularly controversial.

She became the chief of the EPA’s air and radiation office in 2009, which put her in charge of Beale’s work. She attended a retirement party for him in September 2011 but didn’t raise objections when he continued to collect a paycheck — though rarely showed up for work — until a year and a half later.

Internal auditors at the agency say Ms. McCarthy raised her concerns on Nov. 1, 2012, but she waited a few months after that before canceling his recurring 25 percent retention bonus and demanding that he produce documentation of his CIA employment. He resigned a couple of months after that.

Sen. Barbara Boxer, California Democrat and chairwoman of Senate Environment and Public Works Committee, said at a hearing last year that Ms. McCarthy, who has since been promoted to be the agency’s chief, should be praised for her help in uncovering the scheme.

Ms. Boxer’s office didn’t respond to a request for comment Wednesday.

Committee Republicans said Ms. McCarthy should have questioned Beale’s work status earlier.