A method and apparatus for managing separation between vehicles. A closest point of approach between a first vehicle traveling along a first path and a second vehicle traveling along a second path is predicted. A number of compensation commands for altering the first path of the first vehicle are generated using the closest point of approach and a desired level of separation between the first vehicle and the second vehicle. The number of compensation commands is integrated with a number of control commands for the first vehicle to form a final number of control commands configured to maneuver the first vehicle to substantially maintain the desired level of separation between the first vehicle and the second vehicle. A response of the first vehicle to the final number of control commands is a desired response.