Safety is a key performance indicator for the sustainable management of a coastal ferry service business. An efficiency strategy that balances safety and transport performance should be considered. The purpose of this study is to evaluate the relative transport efficiency of coastal ferry operators through undesirable safety-related output. Coastal ferry operators create added value through logistics activities such as cargo and passenger transport. Accordingly, this study designed a three-stage network-slacks-based measure (SBM) model that delineated production through ferry transport services such as service generation, service execution, and transport value creation. Detention records and marine accidents caused by human errors or technical faults were considered undesirable safety-related outputs. Moreover, the relative transport efficiency of 23 Korean firms that have continuously managed a coastal ferry transport business from 2015 to 2018 was analyzed. The results showed that the differentiation of transport efficiency of firms improved when applying the three-stage network SBM model compared to applying the SBM model that did not consider the internal production stage. This fact suggests that it is more desirable to apply the three-stage network SBM model proposed in this study when a more stringent comparison of transport performance is needed in terms of service quality.