Supervisory control reconfiguration can handle the uncertainties including resource failures and task changes in discrete event systems. It was not addressed to exploit the robustness of closed-loop systems to accommodate some uncertainties in the prior studies. Such exploitation can cost-efficiently achieve reconfigurability and flexibility for real systems. This paper presents a robust reconfiguration method based on Petri nets (PNs) and integer programming for supervisory control of resource allocation systems (RASs) subject to varying resource allocation relationships. An allocation relationship is seen as a control specification while the execution processes requiring resources as an uncontrolled plant. First, a robust reconfiguration mechanism is proposed. It includes updating the P-invariant-based supervisor and evolving the state of the closed-loop system. The latter adapts to the control specification changes by the self-regulation of the closed-loop system's state. Next, two novel integer programming models for control reconfiguration are proposed, called a reconfiguration model with acceptability and reconfiguration one with specification correction. Since both models integrate the firability condition of transitions, no additional efforts are required for the state reachability analysis. Finally, a hospital emergency service system is used as an example to illustrate them. (C) 2014 Published by Elsevier Ltd.