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The widespread use of software-intensive cyber systems in critical infrastructures such as ships (CyberShips) has brought huge benefits, yet it has also opened new avenues for cyber attacks to potentially disrupt operations. Cyber risk assessment plays a vital role in identifying cyber threats and vulnerabilities that can be exploited to compromise cyber systems. Understanding the nature of cyber threats and their potential risks and impact is essential to improve the security and resilience of cyber systems, and to build systems that are secure by design and better prepared to detect and mitigate cyber attacks. A number of methodologies have been proposed to carry out these analyses. This paper evaluates and compares the application of three risk assessment methodologies: system theoretic process analysis (STPA-Sec), STRIDE and CORAS for identifying threats and vulnerabilities in a CyberShip system. We …