William E. Weaver, 66, an engineer who worked on pilotless aircraft and missiles for the Navy Department, died of cancer Saturday at his home in the Wood Acres section of Bethesda.

Mr. Weaver was born in Philadelphia, graduated from the Drexel Institute of Technology there, and worked in that area until World War II, when he was commissioned in the Navy.

Following the war, he went to work for the Navy Department. His assignments included the "mothballing" of World War II aricraft and the development of more modern weapons, including guided missiles. He retired in 1972.

Mr. Weaver was an active member of the Metropolitan Memorial United Methodist Church in Washington. He was a member of its board, chairman of its membership committee, and a member of its evangelism and worship committees.

Survivors include his wife, Alice, of the home: two sons, Kent, of Gaithersburg, and Scott, of Yosemite National Park, Calif.: a sister, Anne W. Heitzel, and two brothers, Harry W. and Elmer F., all of Philadelphia, and a grandson.

The family suggests that expressions of sympathy be in the form of contributions to the Memorial Fund of the Metropolitan Memorial United Methodist Church, Nebraska and New Mexico Avenues NW, Washington. D.C., 20016.