CONGOMA has a constitution, which guides its operations. CONGOMA is legally designated as the NGO Coordinating Body by the NGO Act of Parliament.

On top of its hierarchy is the Annual General Meeting (AGM) made up by all its members, which is the supreme authority of CONGOMA. Below the AGM is the Governing Council (GC) comprised of member NGOs elected at the AGM to oversee policy formulation and direction, supervise and monitor the operations of CONGOMA Secretariat. Below the GC are three standing committees: Finance and Administration, Standards and the Programs Committees.

In charge of the day-to-day implementation activities is the Secretariat, which is a team of professional staff.