In this paper, an Adaptive Hierarchical Ant Colony Optimization (AHACO) has been proposed to resolve the traditional machine loading problem in Flexible Manufacturing Systems (FMS). Machine loading is one of the most important issues that is interlinked with the efficiency and utilization of FMS. The machine loading problem is formulated in order to minimize the system unbalance and maximize the throughput, considering the job sequencing, optional machines and technological constraints. The performance of proposed AHACO has been tested over a number of benchmark problems taken from the literature. Computational results indicate that the proposed algorithm is more effective and produces promising results as compared to the existing solution methodologies in the literature. The evaluation and comparison of system efficiency and system utilization justifies the supremacy of the algorithm. Further, results obtained from the proposed algorithm have been compared with well known random search algorithm viz. genetic algorithm, simulated annealing, artificial Immune system, simple ant colony optimization, tabu search etc. In addition, the algorithm has been tested over a randomly generated problem set of varying complexities; the results validate the robustness and scalability of the algorithm utilizing the concepts of ‘heuristic gap’ and ANOVA analysis.