Robert R. Bowie will be deputy director of the Central Intelligence Agency for national intelligence, CIA director Stansfield Turner announced yesterday.

Bowie has been a professor of government at Harvard University since 1957, and founded Harvard's Center for International Affairs. He was assistant secretary of state for policy planning in the Eisenhower administration from 1955 to 1957 and was counselor to the State Department from 1966 to 1968.

Bowie, 67, is the last of the three principal deputies to Turner to be named. The others are E. Henry Knoche, deputy director of central intelligence, and Adm Daniel J. Murphy, deputy for the intelligence community.

Bowie will be responsible for the production of the national intelligence estimates.

According to the sources, Bell then asked for an opinion from Benjamin V. Civiletti, the new assistant attorney general in charge of the Criminal Division. Civiletti, the sources said, concurred in the recommendation by Pottinger and his staff.

The burglary probe, which was triggered by discovery of a previously secret file in the New York field office, dealt a heavy blow to the reputation of the FBI and its director, Clarence M. Kelley. Although the break-ins took place before Kelley became director in July, 1973, he had said that the FBI had ceased the practice of surreptitious entries in 1967.

He subsequently was forced to admit publicly that he had been deceived by his subordinates. After the Justice Department entered the case, a special team of FBI agents was assigned to conduct the probe under Pottinger's direct supervision, bypassing Kelley.

That triggered a number of charges that Kelley was not in effective control of the FBI, and the incident is generally believed to have been a factor in Kelley's decision to retire at the end of this year.