In recent years, maritime transportation has played an important role in global economy development. As a result, ship traffic has become more congested. Moreover, ship navigation is susceptible to weather and environmental conditions, and in some cases, it may become dangerous. Therefore, vessels are subjected to high-risk navigation conditions. To understand the latent risk of ship navigation, this study focused on the actual ship behavior. Thus, an analysis of ship behavior was carried out using historical ship navigation based on automatic identification system data. Consequently, a dynamic analysis of the speed and encounter situation was performed. One of the main results of this work was the understanding of the latent risk involved in ships navigating the Seto Inland Sea, which is one of the most congested routes in Japan. Moreover, the risk areas were obtained, and visualized using a geographical information system. The obtained results can be applied to ensure safe navigation and the development of a safe and efficient navigation model.