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), at least one physical resource block (PRB) information; generating, by the UE, UCI to be transmitted, the UCI being arranged in an order of an index of multiple cells; encoding, by the UE, the UCI; performing, by the UE, a Fourier transform (FT) operation on the encoded 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 based on a PUCCH format associated with the multiple cells and the at least one PRB information.