Piracy and armed robbery continue to pose significant security threats to the shipping industry. This paper presents a real-time threat assessment and crisis classification tool for piracy or armed robbery incidents. The tool is part of a crisis classification module that addresses various categories of security threats. This module is currently being developed as part of the EU-funded research project ISOLA, which aims to introduce an intelligent security superintendence ecosystem. The ecosystem is designed to complement the existing ship security processes and measures applied onboard passenger ships. The tool operates by providing real-time threat classification and subsequent warnings by analysing data collected from the ship’s legacy systems and installed sensors with the utilisation of Bayesian probabilistic techniques, particularly Bayesian Networks. The BN model developed for this purpose is thoroughly examined, and its validation is presented through indicative case studies involving piracy and armed robbery. The main objective is to improve situational awareness, enhance vigilance and early threat detection, and support the decision-making process for the Master and crew, especially under time-sensitive circumstances and stressful conditions.