E. Drexel Godfrey Jr., 59, a former assistant director of the Central Intelligence Agency, died of cancer Friday at his home in Princeton, N.J.

Dr. Godfrey was director of current intelligence of the CIA from 1957 to 1970. He prepared daily intelligence reports for the president and operated the agency's crisis center. He was awarded the Distinquished Intelligence Medal when he left the government.

He joined the faculty of Rutgers University in 1974 and established and directed the graduate program in public administration at its Newark campus. From 1971 to 1974, he served as executive director of the Justice Commission established by the governor of Pennsylvania.

Dr. Godfrey was born in Brooklyn, N.Y. and graduated from William College. He was awarded a Woodrow Wilson fellowship at Princeton University from 1947 to 1950, where he received master's and doctoral degrees. He was a Fullbright scholar and social science research fellow in 1950 and 1951. He then returned to Williams, where he taught political science until he joined the CIA.

Survivors include his wife, the former Lois Shufro Tallman, of Princeton; three sons, E. Drexel III, of Sprucedale, Ontario, Dan, of Aberdeen, S.D., and Peter, of Durango, Colo.; two daughters, Kate Weymouth of Barrington, R.I., and Sue Godfrey of Redlands, Calif., and his mother, Florence Godfrey of Tuscon, Ariz.

The family suggests that expressions of sympathy be in the form of contributions to the E. Drexel Godfrey Jr. Master of Public Administration Program Fund, c/o Provost Rutgers-Newark, 15 Washington St., Newark, N.J., 07102, or to a charity of one's choice.