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The Federal Ministry of Agriculture and Rural Development oversees NAQS as a regulatory body.

In order to promote and regulate sanitary (animal and fisheries health) and phytosanitary (plant health) measures in connection with the import and export of agricultural products with a view to minimizing the risk to agricultural economy, food safety, and the environment, it was created for the harmonization of Plants, Veterinary, and Aquatic Resources (Fisheries) Quarantine in Nigeria.

The major goal of NAQS is to stop the introduction, establishment, and spread of zoonotic illnesses, plant and animal pests, and diseases that affect fisheries and their products.

Along with important stakeholders, NAQS also implements emergency procedures to manage or control new pest incursions or disease outbreaks.