The previous managers have been reassigned.
The shake-up of the system follows embarrassing incidents of controllers sleeping on the job and making errors, raising public jitters about the safety of flying.
After the first few incidents, the top FAA official overseeing air traffic operations - Hank Krakowski - resigned.
The FAA also has set up a five-member independent committee to evaluate the training and job placement of air traffic controllers.
Also, teams of experts are examining several of the agency's more complex facilities, including radar centers in Cleveland and on Long Island in New York, to ensure agency policies are being followed and professional standards upheld.
The Associated Press contributed to this report.