A method and apparatus are provided for allocating code resources to ACK/NACK channel indexes, when UEs need ACK/NACK transmission in a wireless communication system in which a predetermined number of orthogonal cover Walsh codes is selected from among available orthogonal cover Walsh codes, at least one subset is formed, having the selected orthogonal cover Walsh codes arranged in an ascending order of cross interference, subsets are selected for use in first and second slots of a subframe, and the orthogonal cover Walsh codes of the subset selected for each slot and ZC sequence cyclic shift values are allocated to the ACK/NACK channel indexes.