A reconfigurable manufacturing system (RMS) means that it can be reconfigured and become more complex during its operation. In RMSs, deadlocks may occur because of sharing of reliable or unreliable resources. Various deadlock control techniques are proposed for RMSs with reliable and unreliable resources. However, when the system is large-sized, the complexity of these techniques will increase. To overcome this problem, this paper develops a four-step deadlock control policy for the detection and treatment of faults in an RMS. In the first step, a colored resource-oriented timed Petri net (CROTPN) is designed for rapid and effective reconfiguration of the RMS without considering resource failures. In the second step, "sufficient and necessary conditions" for the liveness of a CROTPN are introduced to guarantee that the model is live. The third step considers the problems of failures of all resources in the CROTPN model and guarantees that the model is reliable by designing a common recovery subnet and adding it to the obtained CROTPN model at the second step. The fourth step designs a new hybrid method that combines the CROTPN with neural networks for fault detection and treatment. A simulation is performed using the GPenSIM tool to evaluate the proposed policy under the RMS configuration changes and the results are compared with the existing approaches in the literature. It is shown that the proposed approach can handle any complex RMS configurations, solve the deadlock problem in an RMS, and detect and treat failures. Furthermore, is simpler in its structure.INDEX TERMS Simulation, modeling, deadlock avoidance, colored Petri net, reconfigurable manufacturing system, neural network.