The increased number, speed, and size of ships leads to an increased risk of accidents in ports with restricted navigational areas. A comprehensive risk assessment is required to understand the causal mechanisms involved in accidents. This study investigated the factors causing allision accidents that occurred during ship manoeuvres in the port areas. Nonconformities obtained from 112 allision accident reports were classified qualitatively with the Human Factors Analysis and Classification System for Passenger Vessel Accidents (HFACS-PV) method. Then, temporal and causal relationships between nonconformities were evaluated quantitatively with the DBN method. As a result, the probability of an allision accident and the risk identifying factors (RIFs) affecting allision during port manoeuvres were calculated. Familiarity with the vessel, using the bridge navigation equipment and features of structures in the port area are the riskiest factors leading to allision accidents. The study is thought to contribute at a practical and strategic level to ship owners, ship personnel, pilotage services, port authorities and all relevant stakeholders in understanding the risk of allision accidents occurring in ports and developing preventive regulations.