The Heraklion Archaeological Museum is administered by the Director, Dr Stella Mandalaki. It is organized in six main departments:

- the Department of Prehistoric and Minoan Antiquities (3 archaeologists-curators),

- the Department of Preclassical, Classical, Hellenistic and Roman Antiquities (3 archaeologists-curators),

- the Department of Exhibitions, Communication and Educational Programms, (4 archaeologists-curators),

- the Department of Conservation (7 conservators), the Department of Administrative and Financial Support (7 permanent employees of various specializations),

- the Department of Technical Support and Museography (7 permanent employees of various specializations).