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Recently there has been an increase of interest in the concept of satellite formation flying due to the efficiency gains that can be obtained from using a large number of small crafts instead of one large one. In formation flying it is required that the satellites should fly in specified positions relative to the others and with specified attitudes. For this specific motion pattern it is necessary to design control algorithms which are efficient and easy to implement on board. A cluster of satellites needs to operate autonomously to fulfil the control requirements of a mission without human intervention. An agent based control system is proposed to address the problem. The proposed software architecture allows each satellite to monitor the movements of the other satellites and to communicate and cooperate with others to maintain performance. The collaborative autonomous control system is able to reconfigure sensor and actuator functionality in face of degradation or malfunction. The control architecture is analysed for reliability and logical consistency.