He was 89.
Keeney was called the longest-serving federal prosecutor in U.S. history when he retired last year, The Washington Post reported Monday.
He served as deputy chief of the organized crime and racketeering section, chief of the fraud section and deputy assistant attorney general in the criminal section during his nearly 40 years at Justice.
A Justice Department building in Washington was named after Keeney in 2000.
Early in his career, Keeney served as a top prosecutor for Attorney General Robert Kennedy and helped negotiate a treaty with Switzerland that allowed U.S. investigators to access Swiss bank accounts.
Keeney, who died Saturday, was born in Ashley, Pa., and served in the Army Air Force during World War II. He was shot down early in 1945 during a bombing mission over Germany and was held in a Nazi prison camp until the war ended.
He is survived by five children and four grandchildren. His wife Eugenia died in 1993 after 43 years of marriage.
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