Flanigan was named chairman of New Yorkers for Nixon in 1959 when Nixon was seeking the 1960 presidential nomination. Flanigan became national director of Nixon volunteers in 1960 and Nixon's deputy campaign manager in 1968.
He was named presidential assistant and director of the Council of International Economic Policy in 1972.
Flanigan's talent for advancing business interests in regulatory agencies earned him the nickname "Mr. Fixit" from Time magazine, The New York Times reported Wednesday.
Consumer advocate Ralph Nader once called Flanigan the "most evil" man in Washington for his role in an administration criticized for focusing too much on business interests.
Flanigan is survived by his wife of five years, Dorothea von Oswold, three daughters, two sons and 16 grandchildren, the Times reported.
Flanigan and von Oswold lived in Wildenhag, Austria, and Purchase, N.Y.