Despite an abundance in natural and human resources, Indonesia has not been able to significantly improve the level of water, energy, and food (WEF) security. Challenges in achieving WEF security targets mostly relate to resource mismanagement, lack of coordination, authority imbalance among sectors, and overlapping roles and responsibility among levels of government. The immature process of the decentralization has made these challenges even more complex; it is not easy to unify the vision of local governments (i.e. 34 provinces, 416 regencies, 98 cities) with the Regional Head who is elected every 5 years and sometimes brings different goals and development approaches.The lack of information, awareness, coordination and a common framework to bridge the gaps between national and local governments, jeopardizes the attainment of WEF security targets which have been set in the national long-term planning (RPJPN) and mid-term planning (RPJMN). Unfortunately, this complex issue has not received the attention it deserves, from a scientific perspective nor from a practical implementation point of view such as through laws, policies and planning processes.