The safety assurance of autonomous ship systems is anticipated to present various challenges in the near future, necessitating the establishment of unambiguous procedures and references to facilitate the risk-based design of future ship systems. The International Maritime Organization's (IMO) guidelines, as outlined in the current version of the Formal Safety Assessment (FSA), Goal-Based Standards, and the rules from classification societies lack in detail for the risk-based design of autonomous ship systems. In the meantime, the aviation industry's regulations include more structured techniques for aircraft systems engineering, including a risk matrix that is employed as a benchmark to set the system safety objectives throughout various stages of system design. Consequently, this research suggests a methodology to establish target safety levels for the safety assurance of future ship systems, guided by aviation standards, to support the development of risk-based procedures and regulations that ensure the design of safe autonomous ship systems.