Dr. Rudolph A. Winnacker, 80, retired chief historian in the Office of the Secretary of Defense, died of cancer June 21 at his home in Chevy Chase.

Dr. Winnacker moved to Washington in 1941 and joined the Office of Strategic Services, a forerunner of the Central Intelligence Agency. During World War II he served with the OSS in North Africa and southern Europe.

After the war, he joined the old War Department, where he worked on a history of the Office of the Secretary of War. In 1949, he transferred to the Office of the Secretary of Defense. He retired there in 1973.

Dr. Winnacker's duties included responsibility for the annual report of the secretary. This document is addressed to the president and the Congress and is an account of the secretary's stewardship in the previous year. Dr. Winnacker prepared these reports from 1949 to 1970.

Among the special studies he carried was a history of the Soviet Union's entry into the war against Japan in 1945. This was done in 1955 in connection with the release of documents from the Yalta Conference at which the Soviet Union and the western allies drew up plans for their respective postwar zones of influence in Europe.

Dr. Winnacker also was responsible for the preparation of the official version of the Pentagon Papers, a history of the war in Vietnam. And he wrote the regulations that implemented the Defense Reorganization Act of 1958. This act increased the power of the secretary of defense and centralized direction of research and development programs in the Defense Department.

In addition to preparing publications, Dr. Winnacker was the secretary's representative on the National Historical Publications Commission. This body develops programs for the publication of historical documents of national importance and makes grants to scholars and institutions for this purpose.

Dr. Winnacker was born in Dusseldorf, Germany. He came to this country as a child and grew up in Milwaukee. He graduated from the University of Wisconsin and received a doctorate in history at Harvard University. He taught at the universities of Michigan and Nebraska before moving to Washington.

He was a member of the Cosmos Club.

Survivors include his wife, the former Helen Sellery of Chevy Chase; three sons, Paul, of Berkeley, Calif., George, of Piedmont, Calif., and John, of Columbia, Mo.; and seven grandchildren.