Phytosanitary Certificates: How African Exporters Get Them (2026)

If you export fresh produce, grains, seeds, spices, cut flowers or other plant products, you will almost certainly be asked for a phytosanitary certificate. A phytosanitary certificate is an official plant-health document issued by your country's national plant protection agency, and importing countries use it to decide whether your consignment can enter. This guide explains what it is, what it is not, and how the process works in Nigeria, Kenya, Uganda and Ghana, based on international standards and national agency pages read in October 2026. Procedures change, so confirm with your national agency before each shipment.

What is a phytosanitary certificate?

The international standard ISPM 12, published by the International Plant Protection Convention (IPPC) through FAO, says phytosanitary certificates attest that plants, plant products or other regulated articles meet the importing country's phytosanitary requirements and match the certifying statement. Only public officers who are technically qualified and authorised by the national plant protection organization (NPPO) may issue them. The standard says the certificate should preferably be issued before dispatch, and after dispatch only if all required sampling, inspection and treatment were completed before dispatch and the consignment's phytosanitary security is assured.

It is just as important to know what the certificate is not. ISPM 12 says it should contain only phytosanitary information, with no statements on matters such as pesticide residues, quality or commercial details. So a phytosanitary certificate does not prove your product passes the EU's pesticide limits or aflatoxin rules; those are separate requirements set by the destination market and explained by your buyer.

Kenya's KEPHIS describes the starting point clearly: the exporter obtains the import permit or requirements from the importing country, and inspections are performed against them. Ask your buyer for the written plant-health requirements (and any import permit) before you buy packaging or book freight. Requirements can include a specific treatment, a pest-free declaration or an inspection date, and ISPM 12 says the inspection date must be stated if the importing country requires it.

How to get one in Nigeria, Kenya, Uganda and Ghana

Nigeria (NAQS). The Nigeria Agricultural Quarantine Service (NAQS) plant export guidelines say exporters obtain request forms from designated agricultural quarantine offices, submit the completed forms well in advance and present the consignment for inspection. The certificate confirms that accredited NAQS officers inspected the consignment and found it pest-free at examination, and states whether any treatment was applied. One certificate is issued per consignment. The document says certificates are issued after payment of a "token user fee" but does not state an amount, so we do not quote one. It also warns that exports without a certificate risk being rejected or destroyed on arrival, usually at the exporter's expense. The guidelines PDF carries no date, so confirm the current process with NAQS. For product-specific routes see our guides on exporting ginger from Nigeria and sesame seeds.

Kenya (KEPHIS). On KEPHIS's phytosanitary services page, the steps are: obtain the import permit from the importing country; KEPHIS inspectors visit growers during the growing period to check freedom from specified pests and diseases and safe pesticide use; consignments are inspected at airports, seaports and border posts, visually, microscopically or both, with sample size depending on commodity and volume; and certificates are issued for consignments that meet the standards, while non-compliant material is destroyed or prohibited from leaving. Inspectors check freedom from pests and disease, compliance with maximum residue levels, grading, excess moisture, mechanical damage and proper packaging (labelled, clean and well ventilated). The page does not state fees. See our avocado guide for how this plays out for one crop.

Uganda (MAAIF and UEPB). The Uganda Export Promotion Board page describes a two-stage route. Before exporting, you register with UEPB or UNCCI, obtain a letter to the Ministry of Agriculture, Animal Industry and Fisheries (MAAIF), apply for registration with its Crop Inspection and Certification Department, have your packhouse inspected, fix any non-conformities, and obtain an Export Number. At shipment, you apply for inspection, present the consignment for physical inspection, and obtain the certificate. The page says to allow at least one day for inspection, that grains and tea are inspected in bulk, and that if fumigation is required only a MAAIF certified fumigator may perform it, with a fumigation certificate needed before inspection. The page states an official fee of UGX 5,000; it is undated, so confirm the current fee with MAAIF. MAAIF's ePhyto page says Uganda uses the ePhyto system through its national portal, which gives online access to the certification process. See our vanilla guide for a crop-specific view.

Ghana (PPRSD). Ghana's Ministry of Food and Agriculture page says the Plant Protection and Regulatory Services Directorate (PPRSD), through its Plant Quarantine Division, issues phytosanitary certificates for exported plants and plant products based on ISPMs, inspects and certifies exported produce for both phytosanitary and marketing quality compliance, and applies treatment measures, including confiscation and destruction, to non-compliant exports. Some crops have extra export rules of their own, so check the crop-specific rules, for example in our cashew guide. We did not find an official fee schedule on the pages we read, so none is quoted.

What is ePhyto?

The IPPC says ePhyto is the electronic equivalent of the paper certificate, in a standard XML format, containing all the information of the paper version. The IPPC ePhyto Solution has a central Hub that exchanges certificates between national plant protection organizations, and GeNS, a web-based system for countries without their own electronic system. The IPPC page does not say which countries are connected. Of the four countries in this guide, the only one where we confirmed ePhyto use on an official page is Uganda. Ask your agency whether your destination accepts electronic certificates.

Mistakes that delay or void certificates

• Applying late. Agencies need time to inspect, and treatments such as fumigation must be done before inspection where required.
• Information that does not match the shipment. ISPM 12 says certificates with incomplete, false, conflicting or altered information are invalid, and fraud is treated seriously.
• Expecting a replacement. The standard allows replacement certificates only in exceptional circumstances, such as damage or changed destination, and the original must be returned and cancelled.
• Splitting or mixing lots after inspection. Load the inspected goods as presented.

Frequently asked questions

Who issues a phytosanitary certificate in Nigeria? NAQS, according to its plant export guidelines.

How much does a phytosanitary certificate cost? It depends on the country. The Ugandan page lists UGX 5,000; the Nigerian guidelines mention a user fee without an amount; we found no fee stated on the Kenyan or Ghanaian pages.

Does the certificate cover pesticide residues? No. ISPM 12 says only phytosanitary information belongs on the certificate.

Can I get one before I have a buyer? Certificates are issued per consignment against the importing country's requirements, so you generally need a specific shipment and destination.

Getting started

Register with your national agency, request the importing country's requirements from your buyer, and plan inspection time into your schedule. Create a free Comilmart account to list your products under food and agro, and tell overseas buyers to use request for quotation. Also see our farmers' export guide. Official sources: ISPM 12 (FAO/IPPC), IPPC ePhyto, KEPHIS and Ghana MOFA PPRSD. Rules change, confirm with your national plant protection agency before shipping.