Disruptions of the manufacturing systems caused by the disturbances such as the tool wear, machine breakdown, malfunction of robot or transporter, and so on reduce the productivity as well as increase the cost of product. The conventional manufacturing systems are unable to face with the disturbances by their rigid structure. These systems should be stopped when the disturbances occur. The paper presents an Autonomous Manufacturing System based on Swarm of Cognitive Agents (AMS-SCA) in order to adapt to the disturbances. In the AMS-SCA, the manufacturing system is considered as a swarm of cognitive agents where work-pieces, machines, robots, and transporters are controlled by the corresponding cognitive agents. The system reacts to disturbances autonomously based on the reaction of each agent or the cooperation among them. To develop the AMS-SCA, the disturbances happened in the machining shop were analyzed to find out the corresponding management methods. A test-bed was implemented to prove the functionality of the proposed AMS-SCA.