NAQS is a regulatory agency under the Federal Ministry of Agriculture and Food Security, responsible for the prevention, entry, establishment and spread of foreign pests and diseases of plant, animal and aquatic resources and products into the country to promote sanitary and phytosanitary measures as it relates to import and export of agricultural products with a view to minimising the risk to agriculture, food safety and environment.

To prevent the introduction, establishment and spread of pest and diseases of plant/plant products, animal/animal products and aquatic resource products into and out of the country.

1. Enforce and ensure compliance with laws, regulations and schedules of inspection as well as import permits, sanitary and Phytosanitary certificates for importation of plants, animals and aquatic resources;
2. Intercept and seize all illegal imports and exports of agricultural commodities and regulated materials;
3. Ensure that any plant or plant product, animal or animal products, aquatic resources and its products meant for export or export processing, or producing facility that utilizes raw or semi-processed agricultural products must undergo quarantine inspection and certification before packaging and labelling;
4. Ensure that any plant or plant products, animal or animal products, aquatic resources and its products intended for export must be declared to the Service at least 24 hours before the time of departure;
5. Ensure that any international movement of wood packaging materials including dunnages, crates, pallets shall be subjected to quarantine inspection and certification in compliance with ISPM 15;
6. Ensure that any international movement of used vehicles, machinery and equipment must be subjected to Phytosanitary measures to prevent introduction of quarantine pest;
7. Ensure that all imports of live animals must be subject to quarantine inspection and certification at designated quarantine stations, before release into the national herd;
8. Ensure that all plant pests and disease outbreaks, shall be reported to the Service for investigation, treatment, control, prevention and Service shall inform the Honourable Minister for further necessary action;
9. Enforce compliance with any legislation on disposal of plants, plant products, animal, animal products, aquatic resources and its products, biologics, and regulated articles at the ports of entry and Agricultural Quarantine Stations;
10. Develop pest and animal diseases diagnostic and analytic capabilities and establish laboratories and quarantine stations at such places as may be deemed necessary and encourage and promote activities related to the functions of the Service; with respect to plant, plant products; wild life and wild life trophies and wool product;
11. Ensure compliance of acceptable levels of pesticides, mycotoxin, heavy metals, and other contaminants in agricultural produce meant for export;
12. establish the programmes for setting standards and regulations for the prevention, reduction and elimination of quarantine-able diseases, pests and epidemics caused by these diseases or brought about by these pests;
13. Enforce compliance with laws, guidelines, policies and standards on agricultural quarantine procedure;
14. Coordinate and liaise with stakeholders within and outside Nigeria to ensure compliance with matters of agricultural quarantine standards, regulations and enforcement;
15. Enforce compliance with the provision of international agreements, protocols, conventions and treaties on agricultural quarantine, including forestry, endangered species, plants, plant products, animal, animal products, aquatic resources and its products, biologics, sanitation, marine and wildlife, and such other agricultural quarantine agreements as may from time to time come into force such as International Plant Protection Convention, International Office of Epizootics, etc.;
16. Enforce compliance with regulations on the implementation and exportation of plants, plant products, animals, animal products, aquatic resources and its products, biologics, , wildlife and wild life trophies, and wood products;
17. Conduct agricultural quarantine audit, pest surveys and disease surveillance, containment and eradication programmes of regulated quarantine pests and establish data bank on regulatory and enforcement mechanisms of agricultural quarantine standards;
18. Prohibit the use of processes, equipment and materials that are capable of undermining public health, sanitation, and endangering the agricultural economy;
19. Ensure compliance with agricultural quarantine control measures using the registration, licensing, permits, inspection and certification systems;
20. Enforce compliance through monitoring the agricultural quarantine regulations and standards on plants, plant products, animal, and animal products, aquatic resources and its products;
21. Ensure that agricultural quarantine projects funded by donor organizations and external support agencies are carried out in compliance to regulations in plant health, animal and public health;
22. Develop agricultural quarantine networks, compile and synthesize data on agricultural quarantine measures compliance from all sectors;
23. Enter into agreement with public or private organizations and individuals to develop, utilize, coordinate and share monitoring programmes, research works, data on the effect of various activities as they concern the mandate of the Service;
24. Collect and make available, through publications and other appropriate means and in co-operation with public and private organizations, scientific data and other information pertaining to agricultural quarantine measures and standards;
25. Charge fees for tests, inspection, investigations, diagnosis, treatment, prevention and control and other services performed by the Service;
26. Collaborate with relevant agencies in the conduct of public investigation on epidemic, public health and sanitation occasioned by the spread or outbreak of quarantine-able diseases or pests;
27. Conduct training and development of staff in the relevant area of competence; and of other relevant agencies (national and international) with the approval of the Board;
28. Ensure that authorized officer shall board and inspect any aircraft sea vessels, rail wagons, trucks, or any carriage container, carrying any agricultural product at any of the entry or exit point, such as land borders, interstate control post, airport, sea port, etc.

Refer to the national prohibition list which is domiciled with the Nigeria Customs, however, some commodities are restricted or prohibited by the NAQS for danger of introduction of pest and diseases and for compliance to international standards.