Disagreements among experts in organizing marine security patrols whether a single or multi-agency system is an interesting question. So, this study focused on the problem and investigation of important factors to support decision making. The data collected and explored through focus group discussions and then analyzed using Fuzzy Analytic Hierarchy Process (Fuzzy-AHP) and Dominance-Based Rough Set Approach (DRSA). The results not only show that a single agency system is more critical in managing marine patrol operations in Indonesia, but it also explores the underlying factors as evidence in such a way that it becomes an essential ingredient in formulating a solution strategy. Finally, we recommend a further analysis through other approaches, since there is evidence shown that multi-agency system is still an exciting alternative for marine patrol system.