The organization of NCICD reflects the national importance of the program: nearly all Indonesian ministries and Jakarta City administrative bodies are involved and work under the coordination of the Indonesian Coordination Ministry for Economic Affairs. A Program Management Unit forms the core of the NCICD organization, besides the Coordinating Ministry for Economic Affairs including the Ministry of National Development Planning Agency (Bappenas), the Ministry of Public Works (PU), and DKI Jakarta Provincial Government.

The government of The Netherlands provided funds to involve an expert team from Indonesia and the Netherlands consisting of over 40 technical, financial, urban and organizational experts and engineers from 5 of the major consulting companies in The Netherlands on water management, financial aspects and urban development. Most of the civil engineering work however is done by experienced Indonesian engineers, assisted by Netherlands water management experts.

The plan process is supported by leading Indonesian experts, both private and from the most prominent Indonesian technical university: ITB Bandung.