A method for protecting the transmission of network independent clocking and status information over an air interface (20) between a mobile station (10) and base transceiver station (15) is disclosed. The method involves defining a parallel logical channel (35) between the mobile station (10) and base transceiver station (15) to carry network independent clocking (50) and status information. The network independent clocking (50) and status information are removed from the data stream (90) of the traffic channel (25) and transmitted on the parallel channel (35) over the air interface (20). Alternatively, a buffer (79) may be used in conjunction with or singly to process the data stream (90) of the traffic channel (25) to delete or insert bits or characters to minimize or eliminate the need for network independent clocking information (50).