CISD stresses high priority in transparency and accountability in administration and accounts that ensure good governance of the organization. CISD has three-tier organizational structure, namely: a) General Council, b) Executive Committee and c) General Administration. The General Council comprises a group of highly distinguished professionals of the society. It consists of 33 members and holds at least one general meeting annually. The General Council approves all the activities of the Executive Committee.

The Executive Committee (EC) elected by the members of the General Council for 2 years, consists of 11 members who bring their diverse skills and experience to the governance of CISD. It is the supreme authority to frame policies and guidelines to run the organization. It consists of Chairman (1), Vice-Chairman (1), General Secretary (1), Treasurer (1) and Member (7). The EC holds at least 4 meetings (every 3 months) in a year. The EC has been continuously guiding the organization not only to face the current challenges but also to prepare it to play its due role in upholding its image as one of the leading NGOs. The General Secretary of the EC is also executive head of the organization as the Executive Director. S/he is also the administrative head of the organization, is responsible for overall administration and implementation of its different development programs/projects and related activities. Executive Director runs the day-to-day administrative functions of the organization through Director-Programs. Director-Programs act as Chief of Management and Program Development level in the organization.