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The transport governance in metropolitan area remains complicated. Facing the great transport problems, the metropolitan area needs a collective action to overcome the issue. Therefore, the institutional arrangement in dealing with inter-local government cooperation of regional transport governance is an interesting topic of transportgovernance related research. By aiming in understanding of building the new authority in the phenomenon of inter-local government cooperation and its particular impact on metropolitan transport planning and management, this study uses Jabodetabek region as a case study. The thesis expands the understanding of transport problems, current transport systems, future plan, and transport institution in Jabodetabek area. The analysis shows that there are specific conflicts of inter-jurisdictional cooperation in Jabodetabek. Political situation and regulatory framework are the main barriers in creating regional authority in Indonesia, particularly in Jabodetabek metropolitan area. The basis of the analysis is the institutional design theory. To give more understanding of institutional design of metropolitan transport authority, it also elaborates the inter-local government cooperation theory, inter-jurisdictional conflicts of transport planning, transaction costs theory, and the international experience of transport authority types. Finally, this research confirms that building new transport authority is a highly cost action. It needs law certainty, the in line political drive among stakeholders and good financial supports. To cope with the issue, it needs a further understanding on relation of these factors with institutional design in metropolitan area. This study is expected to add some insight into the characteristics of inter-local government cooperation in metropolitan region.