Disruptions of manufacturing systems caused by unexpected disturbances such as the tool wear, machine breakdown, malfunction of robot or transporter, and so on reduce the productivity, and increase the downtime as well as the cost of products. To cope with these challenges, this paper presents a new method to build an Intelligent Manufacturing System based on Cognitive Agent technology (IMS-CA). In the IMS-CA, work-pieces, machines, robots, and transporters are autonomous entities. The system reacts to disturbances autonomously based on the reaction of each autonomous entity or the cooperation among them. In order to develop the IMS-CA, the disturbances happened in the machining shop for manufacturing the clutch housing products were analyzed to classify them and to find out the corresponding management methods. The system with autonomous architecture was developed based on the cognitive agent technology. A test-bed was implemented to prove the functionality of the developed system.