Since the engine and reduction gear in a naval vessel are usually supported by the mounting system separately, the misalignment between the input shaft of the reduction gear and the output shaft of the engine should occur caused by ship motion. In this study, this misalignment is estimated from the linear static analysis assuming that the phase of movements of the engine and reduction gear at low frequency range is same and the dynamic effect is not affect to them. Through comparing the relative displacement of the engine and reduction gear calculated from linear static analysis to that from dynamic analysis as well as experiment, the assumption in this study could be verified.