The Secretariat was officially inaugurated at its premises on the island of Strömsborg in Stockholm on 20 October 1998. In July 2020 the Secretariat moved to the historical Momma Reenstierna Palace in Södermalm, Stockholm after 10 years in the Old Town of Stockholm and in Räntmästarhuset at Slussplan 9.
The mandate of the Secretariat is as follows:
- to provide technical and organisational support to the Chairman of the CBSS and the structures and working bodies of the Council;
- to ensure continuity and enhanced coordination of CBSS activities;
- to implement the CBSS Information and Communication Strategy;
- to maintain the CBSS archives and information database;
- to maintain contacts with other organisations operating in and around the Baltic Sea region, the national authorities of Member States and the media.
The budget of the core part of the Secretariat is financed by annual contributions from the CBSS Member States according to annual budgets approved by the Committee of Senior Officials.