Secretariats and Coordinating Units provide administrative support to their instruments. Normally the decision-making body of the instrument determines the budget to be allocated to the Secretariat/Coordinating Unit including the number of posts and functions. Where MOUs have dedicated Coordinating Units, they are usually funded by voluntary contributions.

The CMS Secretariat provides secretariat functions for ASCOBANS, the Gorilla Agreement and for those MOUs that have no dedicated Coordinating Unit. The Secretariats of CMS and a number of other UNEP- administered instruments share premises in Bonn, some are administered by UNEP but are located elsewhere (the Raptors and Dugongs MOUs having a Coordinating Unit hosted by the Environment Agency Abu Dhabi in the United Arab Emirates, and the IOSEA Marine Turtles MOU being based in the UNEP Regional Office in Bangkok, Thailand). ACAP, ACCOBAMS and the Wadden Sea Seal Agreement are not administered by UNEP and their Secretariats are based in Hobart (Australia), Monaco and Wilhelmshaven (Germany) respectively.