Methods and apparatus are described for transmitting hybrid automatic repeat request-acknowledgement (HARQ-ACK) bits in a physical uplink shared channel (PUSCH) by a user equipment (UE) in a communication system. A method includes receiving a configuration of a plurality of cells, the plurality of cells being associated with one or more transport blocks; arranging HARQ-ACK bits for the plurality of cells, based on an order of cell indexes and an order of transport block indexes; encoding the arranged HARQ-ACK bits; and transmitting, to a node B, the encoded arranged HARQ-ACK bits in the PUSCH. 2 HARQ-ACK bits for a cell configured with 2 transport blocks are included in the arranged HARQ-ACK bits. The arranged HARQ-ACK bits are encoded by a (32, O) block code in case that a number of the arranged HARQ-ACK bits is 3, O being the number of the arranged HARQ-ACK bits.