The increasing demands for energy efficiency and environmental sustainability in the maritime industry have underscored the critical importance of optimizing autopilot systems, which, despite their significance, are often overlooked in ship energy efficiency management. The objective of this study is to enhance the energy efficiency of ships by focusing on the efficiency of autopilot systems, which play a significant role in the management of energy efficiency. The research emphasizes the need for effective decision support systems for ship operators, not only for optimizing ship speeds but also for making informed operational decisions. By utilizing Fuzzy Fault Tree Analysis (FFTA), the study identifies and prioritizes the causes of efficiency losses in autopilot systems and examines their frequency. Based on expert opinions, the research delves into the complexity of autopilot systems and the interactions among various components. Notably, the study highlights the impact of multiple factors on the efficiency of complex autopilot systems, elucidating their relationships through Minimum Cut Sets (MCS) analysis. Furthermore, attention was drawn to the “Improper Alarm Input” event caused by insufficient knowledge and awareness among ship operators, which hinders the effective use of autopilot systems. The findings demonstrate that decision support systems can increase energy efficiency and contribute to the reduction of operational errors by reducing the human factor, which is 99% effective on the “Inefficient Heading Control System”. Additionally, proper utilization of autopilot systems can lead to a decrease in a ship's carbon footprint and operating costs. Overall, the results can affect strategic decisions in ship energy efficiency management and encourage significant steps toward achieving International Maritime Organization's (IMO) sustainability objectives.