The advent of reconfigurable manufacturing systems (RMSs) has given rise to a challenging problem, i.e., how to reconfigure rapidly and validly a RMS supervisory controller in response to frequent changes in the manufacturing system configuration driven by fluctuating market. This paper presents an improved net rewriting system (INRS)-based method for automatic reconfiguration of Petri net (PN) supervisory controllers for RMS. We begin with presenting the INRS which overcomes the limitations of the net rewriting system and can dynamically change the structure of a PN without damaging its important behavioral properties. Based on INRS, a method for design reconfigurable PN controllers of RMS is introduced. Subsequently, we presented an INRS-based method for rapidly automatic reconfiguration of this class of PN controllers. In the reconfiguration method, changes in a RMS configuration can be formalized and act on an existing controller to make it reconfigure rapidly into a new one. Noticeably, no matter the design or reconfiguration, the expected behavioral properties of the resultant PN controllers are guaranteed. Thus, efforts for verification of the results can be avoided naturally. We also illustrate the reconfiguration of a PN controller for a reconfigurable manufacturing cell.