The real-time inverse estimation of the ocean wave spectrum and elevation from a vessel-motion sensor is of significant practical importance, but it is still in the developing stage. The Kalman-filter method has the advantages of real-time estimation, cost reduction, and easy installation than other methods. Reasonable estimation of high-frequency waves is important in view of covering various sea states. However, if the vessel is less responsive for high-frequency waves, amplified noise may occur and cause overestimation problem there. In this paper, a configuration of Kalman filter with applying the principle of Wiener filter is proposed to suppress those over-estimations. Over-estimation is significantly reduced at high frequencies when the method is applied, and reliable real-time wave spectra and elevations can be obtained. The simulated sensor data was used, but the proposed algorithm has been proved to perform well for various sea states and different vessels. In addition, the proposed Kalman-filter technique is robust when it is applied to time-varying sea states.