The heads of the two new Central Intelligence Agency organizations created by the Carter administration are leaving their jobs, CIA officials said yesterday. But they denied that the changes are part of any shakeup in response to recent criticism of the agency.

Robert R. Bowie, a former State Department official and Harvard University professor, retired yesterday as director of the two-year-old National Foreign Assessment Center and CIA deputy director for national intelligence. Bowie will be 70 years old next week and has been bothered by eye trouble in recent months.

Lt. Gen. Grank A. Camm, chief of the National Intelligence Tasking Office, another Carter administration creation, is leaving to take another post, according to the agency. Camm was in charge of coordinating the intelligence activities of various government agencies. His replacement has not yet been named.

Bowie's replacement as the CIA's chief intelligence analyst is Bruce C. Clarke Jr., an insider who joined the agency more than 26 years ago. The son of the four-star general of the same name who led U.S. troops in World War II and Korea, Clarke left the CIA to work in the Pentagon and Department of Energy under James R. Schlesinger.