The improvement of multimodal logistics transportation systems in developed countries has been developing rapidly to reduce transaction costs and increase competitiveness. However, the development of the multimodal logistic transportation system in Indonesia is still relatively slow. This study aims to assess the multimodal transportation institutional coordination of the multimodal logistics transportation system at Tanjung Priok Port. Institutional coordination analysis was assessed from the Transaction Cost Theory and Principal-Agent Theory (PAT) perspectives. Stakeholder Analysis and Q-methodology are chosen as an analysis tool based on the two theories above. Q-Methodology produces a simpler structure of actor perception called actor perception pattern (PP). The perception pattern represents several actors' main perception themes, which would help the analysis focus on the most significant perceptual themes regarding substantial elements of transaction costs. Stakeholder's analysis explains further the results of Q-methodology by mapping the actor, influence, urgency, and importance. This study found that the actor's perception, which is an element of transaction costs, has hampered the coordination in the logistics transport system at Tanjung Priok port due to conflict of interest and adverse selection of informal institutions. This situation becomes more complicated since a specific institution does not yet cover the coordination between actors in multimodal transportation. Therefore, the study suggests establishing the permanent institution as a coordination and management agency to facilitate the strategic concept of relational contracts in the long term, which is expected to expand and deepen institutional coordination.