This article concerns the development of autonomous ship technology in maritime navigation, which entails safety and risk management challenges. This study aims to compare the risk analyses of two levels of autonomy of seagoing ships – A3-B1 (ships with limited crew) and A2-B0 (ships fully unmanned) – based on the results of a project named SAFEMASS developed by DNV GL company for the European Maritime Safety Agency. In addition, identifying new, emerging risks relating to the functioning of MASS is another research goal. The article uses hazard identification methods (HAZID) and fault tree analysis (FTA). In the case of A3-B1 vessels, the main threats result from reduced situational awareness of operators and dependence on automatic systems. In the A2-B0 model, the most significant risks are communication system failures and a lack of physical supervision of processes. The research results indicate the need to implement additional risk control measures, such as system optimization and improvement of human-machine interfaces (HMI). It is suggested that autonomous and low-emission technologies will develop conceptually in the coming years. Still, the widespread implementation of these technologies will take a long time due to the complexity of the processes and high operating costs. This article emphasizes that implementing autonomous technologies is a promising path for the sustainable development of maritime transport. Still, further research is required, investment in infrastructure is needed, and legal regulations must be adjusted.