A method and apparatus for transmitting control information by an enhanced Node B (eNB) in a wireless communication system supporting Multiple-Input Multiple-Output (MIMO) technology is provided, in which at least one parameter required for initial transmission of User Equipment (UE) is transmitted through a Packet Data Control Channel (PDCCH), at least two codewords are received from the UE and then decoded, one of a plurality of indicators, related to an operation of the UE, is determined based on decoding results of at least two codewords, the determined indicator is transmitted through a Physical Hybrid ARQ indicator channel (PHICH), and at least one codeword is received that the UE generates and transmits based on the parameter required for initial transmission of the UE and the indicator related to the operation of the UE.