The Commission has established a Secretariat at its Headquarters in Hobart, Tasmania. The relationship between the Commission and the Government of Australia in respect of CCAMLR’s operations in Australia is prescribed by the Headquarters Agreement. In collaboration with the Tasmanian State Government, the Australian Government provides office accommodation for the Secretariat.

The Secretariat supports the Commission and the Scientific Committee. Its duties include liaising with Commission and Scientific Committee Members, office bearers and the host county Australia; facilitating communications with and between Members, producing and distributing publications;  receiving and managing scientific CCAMLR data and supporting the work of the Scientific Committee and its scientific monitoring programs; monitoring fisheries operating in the Convention Area, managing the Commission budget, and supporting meetings of the Commission and Scientific Committee. It operates based upon a four-year strategic plan endorsed by the Commission.