Despite advances in automated manufacturing systems (AMSs), faults occur from time to time, which cannot be avoided in a complex real system. A fault is one of the primary causes of failures making some AMS operations unable to complete, and the diagnosis is one of the most important steps in fault-recovery and repair. This work develops a methodology for investigating the behavior of faults on the resources in discrete event systems that are failure-prone. We tackle the fault-tolerant problem and propose a method to make the system able to continue performing its duties, while the failed resources are under a repair and recovery process. In this work, a failure-safe model is proposed and, at the same time, a method for fault recovery and repair of a faulty element is presented without interrupting task processing due to the occurrence of fault to some elements. We use redundant elements to replace the target elements, and these redundant elements are used to do the same work as the target elements do, when faults occur to the target elements. A target element is an unreliable element that is prone to failure. After a faulty target element is repaired and recovered, its failure model is automatically replaced by its repaired model to indicate that the corresponding element has returned to work. The proposed method is tested using an application example. The results show, compared with those obtained by the studies in the literature, that the proposed method has a great performance and outperforms the existing studies.