The Institute of Space Science has six laboratories:
- The High Energy Astrophysics and Advanced Technologies Laboratory
- The Cosmology and Astroparticle Physics Laboratory
- The Theoretical Physics Laboratory
- The Space Plasma and Magnetometry Laboratory
- The Space Applications for Health and Safety Laboratory
- The Gravity, Microgravity and Nanosatellites Laboratory
and the following departments:
- The Department of Technology Transfer and Intellectual Property Management
- The Department of Outreach and Communication
- The Technical, Administrative, Public Aquisitions and Investments Department
- The Planning, Contracting and Monitoring Projects Department
- The Financial Department
- The Accounting Department
- The Legal and Human Resources Department
- Quality Management
- Cabinet of the Directive General