Based on Law on Museums i Rulebook on the method and criteria for connection to the Museum System of the Republic of Croatia, the Croatian Natural History Museum is the parent institution in Museum System for natural history in the Republic of Croatia.

Director of the museum, professor Tatjana Vlahović, PhD, is a member of the Council of the Museum System, and museum advisor Irena Grbac, PhD, is a first-level registrar.

From the Rulebook we highlight:
The bearers of the implementation of the first-level parent activity for museums and open-air museums are the specialized parent museums:
For natural history museums - Croatian Natural History Museum, Zagreb

The parent activity includes:
- professional and advisory assistance to museums and other owners of museum collections and museum materials
- improvement of professional work in museums and raising the level of protection and preservation of museum materials
- harmonization of the work and development of museums and coordination of work in the Museum System
– expert supervision of the museum's work
- other tasks in accordance with the Law on Museums.