An apparatus and method for operating a base station and a mobile station in a communication system are provided. The operation of the base station includes persistently allocating resources to at least one mobile station and transmitting, in a current frame, a control information message including a change counter flag indicating whether persistent resource allocation information, transmitted in a previous frame, is changed. An operation of the mobile station includes receiving a control information message, including a change counter flag indicating whether persistent resource allocation information included in a control information message transmitted in a previous frame is changed, from a base station in a current frame and checking a value of the change counter flag.