Phytosanitary Certificate Nigeria: How to Apply

A phytosanitary certificate is issued by the Nigeria Agricultural Quarantine Service (NAQS) and certifies that your produce is free of the pests and diseases the destination country regulates. You apply through the ePhyto portal at ng.ephytoexchange.org. It is required for agricultural commodities, it is issued per consignment, and NAQS does not publish its fee — see below.

The facts

About that fee

We are not going to tell you what a phytosanitary certificate costs, because NAQS does not say.

NAQS maintains a user-fees page at naqs.gov.ng/user-fees. On 18 September 2026 that page carried three headings —

• PLANT EXPORT USER FEES
• ANIMAL EXPORT USER FEES
• AQUATIC EXPORT USER FEES

— and no amounts under any of them. We checked the page source directly rather than trusting the rendered view: it contains no table elements and no Naira figures anywhere.

Other sites publish a phytosanitary fee. None of them cite NAQS, because there is nothing on NAQS to cite. A number you cannot trace to the agency that charges it is a number that will be wrong at the counter, so budget for this line item but confirm the amount with NAQS before you commit to a buyer’s price.

If you have paid recently, tell us what you were charged and at which office. We will publish a range of reported figures, clearly labelled as reader reports rather than an official schedule, which is a more honest instrument than a single invented number.

Where it sits in the chain

The phytosanitary certificate is one of four quality-assurance documents Nigerian exporters may need, depending on what is in the container:

Dried hibiscus, sesame seeds, ginger, cashew nuts and charcoal are agricultural commodities for this purpose. Processed foods in retail packaging generally are not, and go the NAFDAC route instead. Where a consignment could arguably be both, ask before you ship — a certificate from the wrong agency is the same as no certificate.

The timing trap

A phytosanitary certificate cannot be obtained after the goods have left. The inspection is performed on the consignment itself, so it has to happen while the produce is still in Nigeria and still packed as it will travel. There is no retroactive route.

This is the document exporters lose money on most often, and the reason is commercial rather than regulatory: the buyer’s bank frequently releases payment against the certificate. No certificate, no release — and by then the container has sailed and the leverage has gone.

Apply before the goods are packed for departure, not after.

What it costs you to skip it

An agricultural consignment arriving without a valid phytosanitary certificate can be refused entry, held, treated at your expense, destroyed, or returned, depending on the destination’s rules. Every one of those outcomes is more expensive than the certificate, and most also cost you the buyer.

The portals, honestly

The ePhyto application at ng.ephytoexchange.org is a login screen. It publishes no public guidance on eligibility, steps, documents or timelines, so you cannot plan your application from it — you have to hold an account first. That is a real obstacle for a first-time exporter and we would rather say so than pretend the process is documented online.

NAQS’s laws and regulations are at naqs.gov.ng/laws_and_regulations.

Sources

• NAQS — https://naqs.gov.ng/ — issuing agency, ePhyto and verification portals
• NAQS user fees — http://naqs.gov.ng/user-fees/ — headings present, no amounts published (verified in page source, 18 September 2026)
• Nigeria ePhyto — https://ng.ephytoexchange.org/ — login screen, no public guidance
• NEPC, “Export documents and procedures” — https://nepc.gov.ng/get-started/export-documents-procedures/ — confirms NAQS as the issuer for agricultural commodities and lists the parallel NAFDAC, DVPCS and FPIS documents

Last verified: 18 September 2026. This page is marked NOT CONFIRMED because its central figure is unavailable from the issuing agency, not because we have not looked.