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Abstract Background Corn seeds have a high susceptibility to mechanical damage due to their large size and mass. The main purpose of this study was to evaluate the effects of the cushion box and closed let-down ladder usage in minimizing the negative influence of the free fall on the storage potential of corn seeds. Corn seeds were evaluated for the extent of physiological damage by measuring the seed deterioration by the accelerated aging test (percentage loss in germination in the accelerated aging test), using three drop methods (free fall, with cushion box, and with closed let-down ladder) at three drop heights (5, 10, and 15 m) and five different moisture contents (10, 15, 20 and 25%). Results The drop methods had a significant effect on the storage potential of corn seeds. Sample seeds dropped without a ladder (free fall) had a significantly higher average physiological quality loss of 13.87% (loss in accelerated aging germination). In the use of the cushion box, the average percentage loss in germination was calculated to be 11.38%, which was decreased by about 18% more than the free fall. Sample seeds dropped with the closed let-down ladder had a lower average percentage loss in the germination of 8.78%, which showed that the closed let-down ladder significantly helped to reduce mechanical damage to corn seeds by about 37% comparing free fall and by about 23% to the use of the cushion box. The amounts of loss in physiological quality of corn seeds increased significantly with increasing drop height and moisture content, but the use of the cushion box and closed let-down ladder systems somewhat reduced the adverse effect of the above factors. Empirical models were developed for the dependency of physiological damage to corn seeds due to the impact caused by free fall, on the drop height and moisture content at different drop methods. Conclusions To minimize mechanical damage to seeds as they fall into the bin, a let-down ladder should be installed in the bin so that it can receive seeds from the filling spout with minimum damage.