The digitization of ship environments has increased the risk of cyberattacks on ships. The smartization and automation of ships are also likely to result in cyber threats. The International Maritime Organization (IMO) has discussed the establishment of regulations at the autonomous level and has revised existing agreements by dividing autonomous ships into four stages, where stages 1 and 2 are for sailors who are boarding ships while stages 3 and 4 are for those not boarding ships. In this study, the level of a smart ship was classified into LEVELs (LVs) 1 to 3 based on the autonomous levels specified by the IMO. Furthermore, a risk assessment for smart ships at various LVs in different risk scenarios was conducted The cyber threats and vulnerabilities of smart ships were analyzed by dividing them into administrative, physical, and technical security; and mitigation measures for each security area were derived. A total of 22 cyber threats were identified for the cyber asset (target system). We inferred that the higher the level of a smart ship, the greater the hyper connectivity and the remote access to operational technology systems; consequently, the greater the attack surface. Therefore, it is necessary to apply mitigation measures using technical security controls in environments with high-level smart ships.