EASSI was designed as a voluntary organization drawing its membership from the eight countries and including civil society organizations, departments of governments and individuals who shared in its vision and mission. The launching conference proposed a three-tier structure consisting of the General Assembly, Technical/Steering Committee and the Secretariat. Comprising 12 delegates per country (5 government representatives, 5 NGO representatives and 2 individual experts), the General Assembly was to be convened every 2-3 years and was the overall policy making organ. The Steering Committee composed of 16 members (2 from each country), was conceived to provide technical support to the secretariat as well as executive direction and advice. It was to meet twice a year. And the Secretariat, established to oversee the implementation of EASSI's strategies, would consist of a Coordinator and at least two programme officers.

Over the years, changes have been recommended and implemented on this structure.
In 2003, an external review of the organization and its programmes made important recommendations to have the new structure as below:-

a) General Assembly.
b) Board of Directors.
c) The Secretariat