The activities of the Directorate were carried out by the various Divisions, Units, Ports and Outstation offices viz:
- Director’s Office
- E-Clearance/Statistics Unit
- Quality Management System (QMS)
Divisional Offices
- Export
- Port Chemical, Cosmetics and Medical Devices
- Port Drug
- Port Food
- New Technologies/ Post Port-Clearance
Port Offices in Lagos
- Seaports
- Apapa
- Tincan
- Kirikiri Lighter Terminal
- Lilypond, Ikorodu.
- Airports:
- Lagos – Murtala Mohammed International, Airport,
- Kano –Aminu International Airport, Kano,
- Abuja – Nnamdi Azikiwe International Airport, Abuja,
- Enugu – Akanu Ibiam InternationalAirport, Enugu.
- Outstation Offices:
- Port-Harcourt
- Warri
- Calabar
- Kano
- Abuja
- Enugu
- Kaduna
- Onitsha
- Lekki Deep Sea port
- Land borders:
- Idiroko
- Seme
- Kamba
- Jibiya
- Maigatari
- Illela
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