As can be seen through the continuous research on the Marine Autonomous Surface Ships (MASS) in recent years, several positive as well as optimistic results have been emerged, along with several concerns. In particular, the risk analysis process regarding MASS faces many difficulties as the lack of respective data may lead the estimation of probability or frequency to be extremely uncertain or even biased. To this end, the application of risk informed approaches, that are based on the traditional definition of risk, can be quite misleading. This paper presents a methodology for risk assessment on MASS based on the utilisation of the EAST-BL, a system-based methodology that combines the output of three different networks (i.e., task, social and information) for human and non-human agents of a system to identify hazards and the DNV’s framework for risk assessment from the RBAT study. The objective of the paper is to provide insights regarding the application of EAST-BL on MASS as well as the way that system-based methods can be utilised to enhance the hazard identification and risk assessment processes for MASS.