The Administrative Units of the Agency include the following;

Internal Audit Department

Planning and Quality Management

Department of Legal Affairs

Department of Public Relations and Communication

General Department of Endowments

Investment Department

Department of Endowment (Waqf) Funds Affairs

Department of Endowment Funds (that spends the endowment according to conditions set by the donors)

The Administrative Sub-units of the General secretary of the Agency

Office of the General Secretary

Administrative Units of the Assistant of the General secretary of the Agency for Da'wah Affairs and Mosques

Assistant secretary's Office

Department of Da'wah and Religious Guidance

Mosques' Department

The Administrative Units of the Assistant secretary of the Agency for Islamic Affairs

Department of Islamic Affairs

Department of Research and Islamic Studies

The Administrative Units of the Assistant secretary for Common Services Affairs

Human Resource Department

Department of Financial and Administrative Affairs

Information Systems Department