The Service has three (3) Directorates, Eight Zonal offices, Thirty-Six State Commands  & Federal Capital Territory  and Immigration offices  in the 774 local government areas.
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The  three Directorates are:
1. Finance, Administration & Technical Services.
2. Operations, Passport, Border Patrol, ECOWAS & African Affairs
3. Investigation, Inspectorate and Enforcement

Finance, Administration & Technical Services (FATS)
The FATS directorate is statutorily charged with the responsibility of policy initiation, formulation, articulation and implementation.
It is equally responsible for the financial management, recruitment, discipline, postings, deployments and promotion of officers and men of the Service.

Operations, Passport, Border Patrol, ECOWAS & African Affairs
It is responsible for the provision of various immigration facilities such as:
- Visa
- CERPAC
- Passports

Investigation, Inspectorate and Enforcement
Investigation, Inspectorate and Enforcement is a Directorate of the Nigeria charged with the following responsibilities:

Investigation and Aliens Control :
(i) Detection, Screening and investigation of violations and abuses of
    Immigration Laws and regulations