This paper examines institutional collective action and transaction cost (TC) dilemmas in a self‐organizing policy network involving federal, state, and municipal agencies for waste services in a port and industrial park. A thematic analysis revealed dilemmas in: (a) vertical levels, which lack leadership in industrial waste management due to unclear responsibility delegation across government levels; (b) horizontal levels, reluctant to take responsibilities and define jurisdiction boundaries for efficient waste services; and (c) functional levels, which exhibit fragmented and unaligned action scopes. Transaction costs, stemming from a deficiency in expertise, infrastructure, and organized information regarding companies' waste management, hinder effective programs and policies. Without tackling these challenges and TCs through a governance framework that includes implementation strategies, monitoring, and institutional controls, the self‐organizing policy network is likely to remain stuck in collective institutional inertia.