Since the early ’90s the Portuguese Navy has implemented several measures to improve its navigation safety performance, such as new policies, standard operational procedures, auditing and training programs, revision of course programs and certification requirements. Despite this progress, navigation accidents, remain a significant concern for the Portuguese Navy. Moreover, we still need further understanding of the effectiveness of innovative trends in marine technology over navigation safety. This paper presents an analysis of Portuguese’s naval accidents applying an adapted version of the Human Factors Analysis and Classification System-HFACS framework. Twenty navigation accidents cases were considered. The analysis shows that causality factors with higher relevance are the decision and perceptual errors, non-use or misuse of instruments (Environmental factors), BRM (Personnel factors), inadequate leadership and inappropriate planning (Unsafe leadership). These findings provide an essential contribution to the revision of educational and training programs, insights for the design of bridges and navigation aids.