This paper presents a detailed study of tsunami hazard in ports and its correlation with the damage suffered by marine vessels. The study aims to develop a new loss function to estimate the potential damage of marine vessels due to tsunami attack based on a novel multivariate statistical modeling method, which used several explanatory variables simultaneously to estimate an outcome or the probability of such outcome. In the first part of the paper, tsunami heights and velocities are numerically modeled by using highresolution bathymetry and topography data for the southern part of Honshu Island. We apply statistical methods to the complete sequence of spatially distributed time series of tsunami parameters in order to obtain the best fit with the observed damage data. In the second part, we develop loss functions for marine vessels by using ordinal regression, which uses simultaneously several explanatory variables. We perform several statistical tests to determine the appropriate model variables to be used in developing three-dimensional loss estimation surfaces, which provide probability of loss for each combination of measured or simulated values of tsunami parameters. The main feature of the developed loss functions presented in this study is their capability to integrate the key factors influencing the damage probability, such as tsunami parameters, characteristics of marine vessels and the impact of collision experienced by the vessels during the tsunami. Such a robust method, therefore, is crucially important to understand the tsunami impact on ports and, particularly on marine vessels.