The Secretariat, whose composition shall reflect the AU principle of equitable regional representation, shall be headed by the Executive Secretary, who shall be a senior official from a Member Service and assisted by such number of staff as may be determined by the Conference for the discharge of its duties

It shall be based in Addis Ababa, Ethiopia, and to this end, a Memorandum of Understanding will be entered into between CISSA and the Government of the Federal Democratic Republic of Ethiopia, which will, amongst others, cover the diplomatic privileges and immunities of the staff members of the Secretariat.

The role and functions of the Secretariat shall be to:

• Obtain relevant intelligence reports and data from Members to fulfill its strategic reporting obligations to the African Union Commission
• Submit to the AU Commission Chairperson, relevant decisions resulting from Conferences
• Take part in the activities of the PSC as an organ of the African Peace and Security Architecture (APSA), and share any relevant insights with CISSA Members
• Collaborate with and support the activities of the PSC as the case may be
• Implement any relevant decisions, follow-up plans, monitor programs, actions and strategies of the Peace and Security Council of the AU regarding the intelligence and security matters

• Submit to Members half yearly reports on the state of peace and security on the continent from the perspective of the AU and any other issues relevant to a better appreciation of the state of peace and security
• Develop and host the database of CISSA on all threats on the continent
• Prepare Plan of Action for the Secretariat
• Prepare and manage the budget of the CISSA in accordance with the financial rules of CISSA
• Coordinate the activities of other CISSA bodies.
• Prepare the Continental Intelligence Estimate (CIE)
• Provide strategic assessments to members with regard to peace and security issues on Africa.
• Fulfill any other tasks as may be assigned by the AUC Chairperson and the Conference;