The advent of automated manufacturing systems and the variability in demand pattern have forced the manufacturers to increase the flexibility and efficiency of their automated systems to stay competitive in the dynamic market. Loading decisions play an important role in determining the efficiency of manufacturing systems. Machine loading problems in flexible manufacturing systems (FMSs) are known to be NP-hard problems. Although some NP-hard problems could still be optimized for very small instances, machine loading complexity is so extensive that even small problems take excessive computational time to reach the optimal solution. To ease the tedious computations, and to get a good solution for large problems, this paper develops a special Immune Algorithm (IA) named 'Modified immune algorithm (MIA)'. IA is a suitable method due to its self learning capability and memory acquisition. This paper improves some issues inherent in existing IAs and proposes a more effective immune algorithm with reduced memory requirements and reduced computational complexity. In order to verify the efficacy and robustness of the proposed algorithm, the paper presents comparisons to existing immune algorithms with benchmark functions and standard data sets related to the machine loading problem. In addition proposed algorithm has been tested at different noise level to examine the efficiency of algorithm on different platforms. The comparisons show consistently that the proposed algorithm outperforms the existing techniques. For all machine loading dataset proposed algorithm has shown good results as compared to the best results reported in the literature.