Disruptions in manufacturing systems caused by system changes and disturbances such as the tool wear, machine breakdown, malfunction of transporter, and so on, reduce the productivity and the increase of downtime and manufacturing cost. In order to cope with these challenges, a new method to build an intelligent manufacturing system with biological principles, namely an ant colony inspired manufacturing system, is presented. In the developed system, the manufacturing system is considered as a swarm of cognitive agents where work-pieces, machines and transporters are controlled by the corresponding cognitive agent. The system reacts to disturbances autonomously based on the algorithm of each autonomous entity or the cooperation with them. To develop the ant colony inspired manufacturing system, the disturbances happened in the machining shop of a transmission case were analyzed to classify them and to find out the corresponding management methods. The system architecture with the autonomous characteristics was generated with the cognitive agent and the ant colony technology. A test bed was implemented to prove the functionality of the developed system.