Organisational structure of the HHI is arranged into several departments. Hydrographic activity starts with the survey of the sea, in the internal waters and territorial sea, and the Ecological and Fisheries Protection Zone (ZERP) of the Republic of Croatia, covering a total surface area of about 55,349 km² or 97.9 % of the land area.

Survey operations are carried out chiefly by Hydrographic Department and Oceanographic Department, with the support of s/v Hidra and s/v Palagruža. Nautical Department and Cartographic Department are involved in the field operations conducted in coastal areas. All measured data are stored into modern databases with the support of Information System Department. Cartographic Department and Nautical Department are responsible for the production and maintenance of official nautical charts (paper and electronic ones), and other publications, using advanced computer software. Nautical Department as National Coordinator for Navigational Warnings monitors on a daily basis all the navigational warnings important for the safety at sea. Reproduction Department is responsible for publishing and printing of paper charts and publications.

HHI is registered as a public institution of the Republic of Croatia under valid regulations, which falls within the responsibility of Legal-Personnel-General Services Department, and Accounting-Financial-Sales Department.