An apparatus and method for transmitting Uplink Control Information (UCI) over a Physical Uplink Control CHannel (PUCCH) in a communication system. A method includes acquiring, by a user equipment (UE), from an evolved Node B (eNB), information for a PUCCH format associated with multiple cells; generating, by the UE, UCI to be transmitted, wherein the UCI being arranged in an order of an index of the multiple cells if the PUCCH format is used; modulating, by the UE, the UCI by using quadrature phase shift keying (QPSK); performing, by the UE, a Fourier transform (FT) operation on the modulated UCI; performing, by the UE, an inverse Fourier transform (IFT) operation on the Fourier transformed UCI; and transmitting, by the UE, the inverse Fourier transformed UCI using the PUCCH format based on the information for the PUCCH format.