The governance bodies of the HFSPO are the Board of Trustees, Council of Scientists and the Strasbourg-based Secretariat. In addition to these statutory bodies, the Program is discussed regularly by an Intergovernmental Conference, which decides on the financial framework of contributions by the members.

The members of the HFSPO, the so-called Management Supporting Parties (MSPs) are the contributing countries and the European Commission, which contributes on behalf of the non-G7 EU members.

The current MSPs are Australia, Canada, France, Germany, India, Italy, Japan, Republic of Korea, Norway, New Zealand, Singapore, Switzerland, the United Kingdom, the United States of America and the European Commission.