A method and apparatus for multiplexing positive or negative acknowledgement signals (ACK or NACK, respectively) and channel quality indication (CQI) signals from a user equipment (UE) to a serving base station (Node B) during a CQI transmission time interval (TTI) in a single-carrier frequency division multiple access (SC-FDMA) communication system. The UE does not have simultaneous data transmission. The multiplexing of acknowledgement signals is implicitly achieved by the UE applying different orthogonal covers on the reference signal (RS) symbols transmitted in the CQI TTI, depending on whether the UE sends ACK or NACK. At the Node B receiver, the detection of ACK or NACK is based on the accumulated RS energy, after removing each of the possible orthogonal covers applied at the UE transmitter. For robust system performance, absence of ACK/NACK and NACK are mapped onto the same orthogonal cover.