The tsunami caused by the Tonga submarine volcanic eruption that occurred at 13:15 Japan Time (JST) on January 15, 2022, exposed a blind spot in Japan’s tsunami monitoring and warning system, which was established in 1952 for local tsunamis and expanded to distant tsunamis after the 1960 Chile tsunami. This paper summarizes how the warning system responded to the unprecedented tsunami, the actual evacuation process, and the damage it caused in Japan. Initially, the tsunami from the volcanic eruption was expected to arrive at approximately midnight with amplitudes of less than 20 cm. However, a series of short waves arrived at approximately 21:00, a few hours earlier than expected. The early arrival of these sea waves coincided with a rapid increase in atmospheric pressure; then, the short-period component was predominant, and the wave height was amplified while forming wave groups. After a 1.2 m tsunami was observed in Amami City in southern Japan at 23:55 JST, the Japan Meteorological Agency issued a tsunami warning/advisory. The tsunami continued, and all advisories were cleared at 14:00 JST on January 16. Information about this tsunami and the response to it are summarized here, including the characteristics and issues of the actual tsunami evacuation situation in each region. There were no casualties, but the issues that emerged included difficulty evacuating on a winter night and traffic congestion due to evacuation by car and under the conditions of the COVID-19 pandemic. In the coastal area, damage to fishing boats and aquaculture facilities was reported due to the flow of the tsunami. In addition, damage to aquaculture facilities, including those producing oysters, scallops, seaweed and other marine products, decreased the supply of marine products, and the economic impact is likely to increase in the future.