The operation of ship especially Ro-Ro ferry contributes much to support connectivity among islands for a country like Indonesia which has categorized as archipelago country. The reliability of Ro-Ro ferry operation will impact to the movement of cargo as well as passenger and later it could cause larger impact on the economic sustainability of region involved. The reliability of Ro-Ro ferry operation could be determined by operation function such ferry. One important function is ship handling function which consists of the interaction among human, technical, environment, management and weather. As the consequence to perform the objective of ship handling, the hazards might appear. It could be remarked that ferry accidents often occur during their service e.g. collision, grounding, sinking and contact. Such accident may be as part of the result of ship handling difficulty as part of ship handling function. Therefore, decision tool model based on the ship handling difficulty need to be developed. The first aim of this paper is to present the proposed ship handling model through the combination of Analytic Hierarchy Process (AHP) and Fuzzy Inference System (FIS). The second aim is to perform a simulation to compare the ship handling difficulty level for Ro-Ro ferry at several straits in Indonesia. The result of this research might be used by ship masters, shipping companies and port authorities to develop strategies in overcome the hazard of Ro-Ro ferries so the reliability of ferry operation could be maintained.