This paper deals with the partial reconfiguration of the discrete control systems due to resource failures using the structural redundancy of the global system model. The approach herein proposed introduces a new subclass of Interpreted Petri Nets (IPN), named Interpreted Machines with Resources (IMR), allowing representing both the behaviour of a system and the resource allocation. Based on this model, an efficient reconfiguration algorithm is proposed; it is based on finding the set of all redundant sequences using alternative resources. The advantages of this structural reconfiguration method are: (1) it provides minimal reconfiguration to the system control assuring the properties of the original control system, (2) since the model includes resource allocation, it can be applied to a variety of systems such as Business Processes, and FPGAs, among others. The method is illustrated through a case study dealing with a manufacturing system controller that includes both alternative resources and operation sequences.DOI: http://dx.doi.org/10.5755/j01.itc.44.3.8783