NAPTIP is one of the agencies under the supervision of the Federal Ministry of Justice. The Act establishes a part time Governing Board which consist of-
i. A Board Chairman who shall be a person with knowledge and experience in matters related to counter-trafficking in persons.
ii. Two representatives of Civil Society Organizations involved in matters relating to trafficking in persons.
iii. A representative from each of the following Institutions or Agencies who shall be within the Directorate cadre-
- Federal Ministry of Justice
- Federal Ministry of Women Affairs
- Federal Ministry of Labour and Productivity
- Nigeria Police Force
- National Intelligence Agency
- Nigeria Immigration Service
- National Planning Commission
- The Director-General, who is also the Chief Executive Officer and Chief Accounting Officer of the Agency shall be the Secretary to the Board
The Agency performs its functions through 8 Specialized Departments, 5 Units and has Zonal Commands covering the geo-political zones of the country.
- Investigation and Monitoring.
- Legal and Prosecution.
- Counseling & Rehabilitation.
- Public Enlightenment.
- Research and Programmes Development
- Training and Manpower Development.
- Finance and Accounts.
- Press and Public Relations.
- Intelligence and International Cooperation.
At present there are 9 Zonal Commands located in Lagos, Benin, Enugu, Uyo, Sokoto, Kano, Maiduguri, Osogbo and Makurdi. The Agency also has a liaison office in Port-Harcourt.
The Headquarters in Abuja and All the Zonal Commands have transit shelters which were created to cater to the physical and psychological well-being of victims of trafficking.