Human is a key element of the safety of life on board ships and a significant contributing factor to most of the accidents and incidents in the maritime industry. At this point, risk analysis plays a critical role in ensuring operational safety and maritime transportation sustainability. This paper aims to systematically evaluate how human errors (HEs) contribute to operational risks. Based on this, Fault Tree Analysis (FTA) is combined under an Interval Type-2 Fuzzy Logic environment with Success Likelihood Index Method (SLIM). Whilst the FTA evaluates the criticality of the operational activities, the Interval Type-2 Fuzzy Sets (IT2FS) deals with vagueness and subjectivity in using experts’ judgements, and the SLIM estimates the probabilities for the human error-related basic events. Since container losses can lead to severe damage and catastrophic events in a container terminal, loading operation was investigated as a case study. Safety culture, experience, and fatigue were observed as highly effective factors in crew performance. The obtained results also indicate that this hybrid approach can effectively be applied to determine the operational vulnerabilities in high-risk industries. The paper intends to improve safety control levels and lower losses in the future of maritime container transport besides emphasising the potential consequences of failures and crucial human errors in the operational process.