In his Swiss cheese model, Reason states that no one can foresee all possible accident scenarios. If holes can be visualized and the relationship between holes and latent conditions can become clear, then it is possible to control the occurrence of holes. The objective of this research is to determine the relationship between latent conditions and the characteristics of holes. In this study, 84 serious marine accidents, divided into six types, were analyzed. Furthermore, the safety management system (SMS) in organizations and risk management at local workplaces were considered as defensive layers, and 10 latent conditions were defined by modifying the software-hardware-environment-liveware (SHEL) model. The following results were found. Holes in the SMS defensive layer tend to arise during the early stages of the plan-do-check-act (PDCA) cycle, except for cases involving sinking. Holes in the defensive layer of risk management tend to arise during the early stages of the risk management process in cases involving collisions, occupational casualties, fire, or explosion. The most frequent latent condition was an inadequate condition of operators, but was not necessarily the same for different types of accidents. These findings indicate that the locations of and reasons for the opening of holes can be determined. By applying a method for closing holes in combination with the findings of this study, accidents can be systematically prevented.