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), information for configuration of a first PUCCH format and a second PUCCH format; selecting, by the UE, one of the first PUCCH format and the second PUCCH format, wherein the second PUCCH format is selected, by the UE, for multiple cells from an evolved Node B (eNB); generating, by the UE, UCI to be transmitted; encoding, by the UE, the UCI; performing, by the UE, a Fourier transform (FT) operation on the encoded UCI if the second PUCCH format is selected; performing, by the UE, an inverse Fourier transform (IFT) operation on the encoded UCI or on the Fourier transformed UCI; and transmitting, by the UE, the inverse Fourier transformed UCI using the selected PUCCH format.