This study investigated navigation safety in Taiwanese harbors and surrounding waters. The key factors that influence navigation safety were summarized by reviewing relevant literature and by interviewing experts. A questionnaire survey was used to assess the degree of importance of these different factors, including human, vessel, harbor traffic, and climatic and environmental factors. A factor analysis was used to design a systematic hierarchical structure for clustering these factors. This study suggests that duty officers can prevent maritime incidents from occurring by taking precautions against the various key factors identified here.