A Permanent International Secretariat of the CBSS was established following a decision taken at the 7th Ministerial Session of the CBSS in 1998 in Nyborg, Denmark. The Secretariat was officially inaugurated at its premises on the island of Strömsborg in Stockholm on 20 October 1998. In November 2010 the Secretariat moved in to its new premises located 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 CSO. Since its establishment in 1998, the following specialised units have been integrated to the Secretariat: January 2001 – the Baltic 21 Unit (servicing the Baltic 21 Network) and March 2002 – the Children’s Unit (servicing the Expert Group for Cooperation on Children at Risk) and the Task Force against Trafficking on Human Beings.