The supreme organ of CHAZ is the General Annual Council which convenes once annually. The Council consists of the following entities:

• Two representatives from each Constituent Member
• One representative of each Health Centre or Church Based Community Health Programme who are paid up members. 
• Two representatives each from a hospital which is a paid up member.

Board members of CHAZ are elected by the Annual General Council at the annual meeting. Approval of decisions on matters of policy are deemed effective and sufficient if two thirds majority of the constituent members of CHAZ vote in favour thereof.

There is a Members Forum which comprises one representative leader from each Constituent Member of CHAZ. The Members Forum function on an ad hoc basis and play an advisory role to the Board in respect of matters either referred to it by the Board or which the Members Forum consider necessary in the interest of CHAZ to address in between Annual General Councils.

The Board is responsible for ensuring that the decisions of the Annual General Council are carried out and oversee the management of CHAZ. It is the policy making body of CHAZ and is responsible for giving direction to CHAZ. The numerical composition of the Board is nine excluding the Executive Director who is an ex officio member and secretary of the Board. The ninth member of the Board is a legal expert. The Board is elected for a term of two years. The Board elects among their number the Executive that is, the Chairperson, the Vice chairperson and the Treasurer. Board meetings are held on a quarterly basis.

The Board is responsible for the following:

• Resource mobilization and donor relations
• Employment, remuneration and termination of secretariat staff and other matters incidental thereto.
• Approval and review of work plans, reports and budgets.
• Approval and ratification of contractual agreements entered into on behalf of CHAZ.
• Appointment of auditors for the purpose of the audit of the CHAZ books of accounts.
• All property of the Association and the income arising therefrom and/or any other source is under the control of the Board for and on behalf of CHAZ.
• The performance of such other functions necessary for the proper running of the association in the interest of CHAZ.

The Board may by resolution in writing delegate such of its functions as deemed necessary to the secretariat while maintaining supervisory role.