The CMS Secretariat is the Convention's coordinating body. Its functions are set out in Article IX of the Convention. They include
- Organize and service meetings of the Conference of the Parties (COP), the Scientific Council (ScC) and the Standing Committee (StC),
- promote and support the development of Agreements,
- stimulate and supervise research and conservation projects,
- promote the exchange of information between the Parties and
- liaise with international governmental and non-governmental organizations.
The CMS Secretariat is provided and administered by the United Nations Environment Programme (UNEP).
Since its establishment the Secretariat has been located in Bonn, Germany. After having been co-located with the Federal Agency for Nature Conservation (BfN), the Secretariat relocated to the United Nations Campus in Bonn in 1998. The premises are shared by a number of UN Agencies, such as: UN Volunteers (UNV), the Secretariat of the Framework Convention on Climate Change (UNFCCC) and the Secretariat of the Convention to Combat Desertification (UNCCD).
The Secretariat also has staff outside of Bonn.
CMS Office - Abu Dhabi oversees implementation of the Memorandum of Understanding on the Conservation of Migratory Birds of Prey in Africa and Eurasia (Raptors MOU), and the Memorandum of Understanding on the Conservation and Management of Dugongs and their Habitats throughout their range (Dugong MOU). The office addresses common threats to migratory species of regional interest, such as marine mammals and marine turtles in relation to by-catch and entanglement, and promotes CMS and its agreements in the West Asian and North-west Indian Ocean regions. Established in 2009, the office is hosted by Environment Agency - Abu Dhabi, on behalf of the Government of the United Arab Emirates.