The Agency has the following structure:
- The Headquarters (located in the Federal Capital Territory, Abuja)
- Six Departments
- Geoscience, Planning & ICT
- Regional Geology
- Economic Geology
- Applied and Engineering Geology
- Administration and Finance
- Geophysics
- Four National Research Centres:
- National Geosciences Research Laboratory, Kaduna, Kaduna State.
- National Centre for Marine Geosciences, Yenegoa, Bayelsa State
- National Geohazard Monitoring Centre, Awka, Anambra State.
- National Geosciences Information Centre, FCT, Abuja.
- Six Zonal offices, Twenty Seven State Offices.
- FCT
- South West Zone
- Lagos
- Ogun
- Oyo (Zonal Office)
- Osun
- Ondo
- North West Zone
- Sokoto (Zonal Office)
- Zamfara
- Kano
- Kaduna (NGRL)
- North Central Zone
- Kwara
- Benue
- Plateau (Zonal Office)
- Kogi
- Nasarawa
- Niger
- North East Zone
- Adamawa
- Bauchi
- Borno (Zonal Office)
- South South Zone
- Bayelsa (NCMG)
- Benin (Zonal Office)
- Delta
- Cross-River
- South East Zone
- Anambra (NGMC)
- Enugu (Zonal Office)
- Ebonyi
- Imo