There is increasing concern over the possibility of the occurrence of huge Toukai, Tonankai, and Nankai earthquakes in the Nankai Trough, located in the Pacific Ocean off Japan. It is estimated that there is a 50% probability of a tsunami being generated by an earthquake in this area over the next 30 years. A tsunami attack on the coast of Japan would not only increase the sea level, but would also create strong horizontal flows in bays and ports. In particular, along the coastal area of Osaka Bay, Japan, there are numerous small ports where pleasure ships and/or fishery boats are moored. Any small ships moored in these ports would be subject to violent motion by strong lateral flows, even if they are moored to each other. As a consequence, the mooring lines would be cut, ships would move uncontrollably, and causing damage to facilities. Thus, it is very important from the viewpoint of marine-disaster prevention to gain a better understanding of the motion of small vessels originating in tsunami flows and to develop countermeasures in the face of a tsunami attack. In this paper, basic analyses of the ship motions resulting from a tsunami attack are carried out, and possible countermeasures are investigated. First, we describe mathematical models approximating the flow of tsunami and the abrupt maneuvers of relatively small vessels while being moored. Next, numerical simulations of the lateral motion of moored ships resulting from a tsunami attack on a fishery port located in the Osaka Bay are carried out. Additionally, the possibility of relatively high tension to be generated along the mooring lines is evaluated. Finally, the results of computer simulations demonstrate that such hazardous phenomena can be addressed with appropriate countermeasures.