The technical difficulty of balancing large data capacity with a high data transfer rate in holographic data storage systems (HDSSs) is significantly high because of tight tolerances for physical perturbation. From a system margin perspective in terabyte-class HDSSs, the positioning error of a holographic disc should be within about 10 µm to ensure high readout quality. Furthermore, fine control of the positioning should be accomplished within a time frame of about 10 ms for a high data transfer rate of the Gbps class, while a conventional method based on servo control of spindle or sled motors can rarely satisfy the requirement. In this study, a new compensation method for the effect of positioning error, which precisely controls the positioning of a Nyquist aperture instead of a holographic disc, has been developed. The method relaxes the markedly low positional tolerance of a holographic disc. Moreover, owing to the markedly light weight of the aperture, positioning control within the required time frame becomes feasible.