In this paper, a method to determine the optimal configuration of operating policies in an integrated-automated manufacturing system using the Taguchi method and computer simulation experiments is presented. An integrated-automated manufacturing system called direct-input-output manufacturing system(DIOMS) is described. We only consider the operational aspect of the DIOMS. Four operating policies including input sequencing control, dispatching rule for the storage/retrieval(S/R) machine, machine center-based part type selection rule, and storage assignment policy are treated as design factors. The number of machine centers, the number of part types, demand rate, processing time and the rate of each part type, vertical and horizontal speed of the S/R machine, and the size of a local buffer in the machine centers are considered as noise factors in generating various manufacturing system environment. For the performance characteristics, mean flow time and throughput are adopted. A robust design experiment with inner and outer orthogonal arrays are conducted by computer simulation, and an optimal configuration of operating policies is presented which consists of a combination of the level of each design factor. The validity of the optimal configurations is investigated by comparing their signal-to-noise ratios with those obtained with full factorial designs.