Roughly 2 decades ago, the Indonesian Decentralization Act 22/1999 (revised by Act 32/2004 and Act 23/2014) initiated a remarkable shift in the governance system for Indonesia: from a strongly hierarchical system to a further decentralized one. The shift has created fragmented governance for metropolitan transportation planning. Consequently, Indonesian metropolitan areas have experienced increasing transaction costs in policy coordination and difficulties in supplying sufficient transport infrastructures. Earlier research has pointed to a range of possible solutions, including strengthening local government capacity. This paper sets out to identify current perceptions regarding transaction costs in Indonesian metropolitan transportation planning. To what extent do high transaction costs create fragmented planning? Have planning actors’ perceptions changed over time? Using Q-methodology and in-depth interviews, the research identifies significant changes in actors’ perceptions, mainly towards the need to establish supraregional institutions and regional development priorities. The findings are critical for institutional reformulation to support comprehensive transportation planning at the metropolitan level.