The bodies of NSDI are comprised of: The NSDI Council, NSDI Board and Workgroups.
 
NSDI Council is a body which implements the National Spatial Data Infrastructure within the Republic of Croatia and coordinates the activities of NSDI subjects within the scope and with rights and obligations determined by the  Law on State Survey and Real Estate Cadastre (NN 16/2007 and 124/10)
 

NSDI Board  is comprised of:

• three representatives of the NSDI Council,
• two representatives of the State Geodetic Administration,
• Heads of workgroups appointed by the NSDI Council.

There are six implemented workgroups at the operational level, dealing with specialized tasks:

• Head of the workgroup for NSDI technical standards,
• Head of the workgroup for NSDI data sharing,
• Head of the workgroup for linking the NSDI program with e-Government,
• Head of the workgroup for NSDI capacity building,
• Head of the workgroup for construction of the NSDI business model,
• Head of the workgroup for NSDI spatial data

Besides the workgroups, there are many projects at the operational level dealing with specific tasks and questions within the scope of NSDI.
State Geodetic Administration manages the tasks of the NSDI Council Secretariat, coordinating all NSDI bodies and providing technical support.