There are many factors affecting navigational safety in ports, including weather, the characteristics of the channels and vessel types, etc. This paper aims to identify the factors influencing navigational safety in ports and to analyze the extent to which such factors affect the safety of ports from the perspective of ship captains through a real case study. A quantitative analysis is carried out using the data collected from 21 captains who have over 10 years experience in operating ships individually. The identified factors indicate risk implications in ports. A fuzzy analytical hierarchy process is used to evaluate the importance of the factors and to rank the safety levels of the targeted ports in Korea from a captain's perspective. Consequently, among Busan, Ulsan, Gwangyang, Incheon, and Mokpo, Busan is evaluated by captains as the safest port, while Mokpo is the most risky. The research also reveals that it is applicable to use domain expert knowledge when historical failure data is unavailable or difficult to access to evaluate port safety. The result shows great research significance in terms of providing relevant stakeholders, such as port authorities and shipping companies, with an insight into port safety performance and thus facilitating the development of the associated risk control measures.