AFoCO spearheads intergovernmental collaboration and coordination through the Assembly, the highest decision-making organ of AFoCO composed of Representatives appointed by the Parties to the Agreement on the Establishment of AFoCO. The Assembly is convened at least once a year in a regular session.

During the session, the Secretariat submits an annual work plan, budget, and progress report for consideration by the Assembly. The executive director heads the Secretariat and is supported by the vice executive director and professional and general staff. The Secretariat introduces official documents, prepares draft decisions, and provides clarifications when questions from the floor are raised.

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