The two levels of the organizational structure of the Environmental Fund are defined as follows:
- Administration Committee: it is the highest authority and exercises the executive level or ruler of the Environmental Fund; establishes mission, defines policies and objectives and therefore is responsible for the decision, guidance and funding approval of plans, programs, projects and the Environmental Fund budget.
- Executive Secretariat: the executor level is composed of a minimum administrative and financial structure and a technical team working directly with the Ministry of Environment. The Executive Director, appointed by the CAFA, is responsible for the management and control of the resources of the Environment Fund.
El Director Ejecutivo, nombrado por el CAFA, es responsable del manejo y control de los recursos del Fondo Ambiental.