An apparatus and method for preventing the disruption of Fiber Channel Fabrics caused by ReConfigure Fabric (RCF) messages is disclosed. The apparatus includes a storage area network and a plurality of Fiber Channel Switches arranged in a Fabric. Each of the plurality of Switches includes logic to selectively configure their Ports to either reject or accept RCF messages. When configured to reject RCF messages, the Switch Port that receives an RCF message will generate a reject message along with a reason code explanation “E_Port Isolated”, and then transition into an Isolated state. When the Switch that generated the RCF message receives the reject message, its Port also transition into the Isolated state. In accordance with the method of the present invention, either a Storage Service Provider or a client can access the Switches of the Fabric through either a command line interpreter or a management application. Once access to the Fabric is established, the logic of the Ports of the Switches can be selectively configured to reject or accept RCF messages as described above.