This paper focuses on how fragmentation in public administration has become a major institutional constraint on CO2 emission mitigation policies in Thailand, particularly for energy policy in the transportation sector. Most of our data are narratives and descriptions derived from in-depth interviews with various governmental agencies and academics. It was found that in practice, the environmental policy link between separated sectors continues to be weak because of the lack of appropriate institutional structure for integration. We conclude that the institutions tend to be independent, fragmented, and working on relatively narrow mandates. The closed decision-making processes and the organizational structures strongly bias the different administrative units towards their respective interests.