The church is further divided into twenty four dioceses, each under the supervision of a bishop, including one diocese encompassing Jaffna, Sri Lanka. The dioceses are governed by diocesan councils composed of all clergy in the diocese as well as lay people elected from the local congregations.Each church will have representation in diocesan council based on their membership. The diocese is headed by the Bishop, who is a presbyter elected through the Diocesan Council. He is considered as the head of the diocese and all the institutions belonging to the diocese. Other than the Bishop, the following are the important administrative posts of each diocese:

• Clergy Secretary : Manages all the activities of the pastoral & evangelical workers in the diocese
• Lay Secretary : Manages all the lay workers' activities in the diocese
• Educational Secretary : Manages all educational institutions and the workers of those institutions
• Diocesan Treasurer : Manages all the income and expenditures of the diocese.

The Diocesan Council also consists of Diocesan Executive Committee, Diocesan Standing Committee, and Pastorate Committee.