Phytosanitary Certificates and Plant Import Permits Explained

A phytosanitary certificate is an official document, issued by the exporting country's national plant protection organization (NPPO), stating that a consignment of plants, plant products or other regulated articles has been inspected or tested and meets the plant health requirements of the importing country. The key takeaway for shippers: the importing country decides whether you need one, the exporting country's government issues it, and neither the shipper nor the forwarder can create or sign it. Many imports also need a separate import permit from the destination country before the goods are shipped. This guide covers the certificate, the US permit system run by USDA APHIS, electronic certificates (ePhyto), inspection at the port of entry and what happens when cargo does not comply. Wood packaging and food have their own regimes, covered in our guides to ISPM 15 wood packaging rules and FDA prior notice and FSVP.

What a phytosanitary certificate is, and what it is not

The certificate comes out of the International Plant Protection Convention (IPPC), a treaty administered under the FAO. The international standard that governs it is ISPM 12, "Guidelines for phytosanitary certificates". In substance, the standard says that certificates are issued by the NPPO of the exporting (or re-exporting) country, on the basis of inspection and, where relevant, testing or treatment, and that they are issued before or at the time of export. They describe the consignment's phytosanitary status at the moment of certification and should not be altered after issue.

The model certificate in the standard asks for details such as the exporter and consignee, the number and description of packages, the place of origin, the declared means of conveyance and point of entry, the product name and quantity, the botanical name of the plants, any additional declaration the importing country demands, and any disinfestation or disinfection treatment. Many certificates will be in the exporting country's own layout, but they follow that model.

Three misconceptions are worth clearing up early:

• It is not a certificate of origin. A certificate of origin proves where goods were made for duty purposes (see free trade agreement certificates of origin). A phytosanitary certificate says nothing about duty or origin rules; it speaks only to pests and plant health.
• It is not a guarantee of entry. The certificate is one condition among several. The importing country still inspects at the border and can refuse, treat or order re-export of a consignment that arrives with a valid certificate but fails inspection.
• It is not only for live plants. ISPM 12 says importing countries should require certificates only for regulated articles, but it also recognises that certificates may be used for some processed plant products that can still carry pests by their nature or processing, with wood and cotton given as examples. Whether your product needs one is the importing country's call.

Who issues it, and who actually does the work

Only the exporting country's NPPO (or officials it authorises) can issue the certificate. In the United States that is USDA APHIS. In other countries it is typically the agriculture or plant protection ministry or an agency under it. The exporter, or a forwarder or agent acting on the exporter's behalf, applies to the NPPO, the goods are inspected (and treated if required), and the certificate is issued.

A forwarder cannot issue, correct or "fix" a certificate. What a forwarder can do is make sure the information on it matches the booking and the rest of the paperwork, because a mismatch is a common reason for a hold at the destination. The details to check before the certificate is issued:

• Consignee name and address, exactly as on the commercial invoice and bill of lading
• Product description and botanical name, consistent with the HS code on the declaration (see how to find the correct HS code)
• Quantity and packaging, matching the packing list
• Container number and seal, where the importing country wants them on the certificate
• Any treatment details (type, date, chemical and concentration) and any additional declaration the importing country's permit requires

Many importing countries also set a validity window between issue and export or arrival, so a certificate issued too early can be rejected. Check the window in the importing country's requirements rather than assuming one.

What triggers the requirement: check the importing country first

The IPPC sets the framework, but each importing country writes its own rules and keeps its own list of what needs a certificate, a permit, a treatment or nothing at all. The right sequence is always the same: identify the commodity, identify the destination, and look up the destination's import conditions before the goods are packed, not after they are booked.

This table is a starting map, not a rule set. Conditions change by commodity, by country of origin and over time, and a single line in a database can turn on the botanical species or the form of the product (fresh, dried, cut, processed). If the lookup is ambiguous, ask the destination's plant health authority before shipping, and ask a licensed customs broker (see do you need a customs broker) to confirm how the permit and certificate will be presented at clearance.

US imports: permits, PPQ 587 and the ACIR database

For goods entering the United States, the certificate and the permit are two separate things. The certificate comes from the origin country's NPPO. The permit comes from APHIS to the US importer, before shipment.

• PPQ 587 is the import permit application for plants and seeds for planting (propagation). APHIS states that most plants and seeds for planting need this permit. Since September 2021 the application has been filed through APHIS eFile rather than the older ePermits system. APHIS warns that processing can take up to two months, so the permit has to be planned with the exporter well ahead of the ship date.
• Fresh fruits and vegetables are covered by 7 CFR 319.56-3, which sets a general permit requirement with exceptions (for example for dried, cured or processed produce). The commodity-specific answer, including any treatment or inspection conditions, is in ACIR.
• ACIR (Agricultural Commodity Import Requirements) is APHIS's search tool for entry requirements. It replaced the older Fruit and Vegetable Import Requirements (FAVIR) database and three manuals (Cut Flowers and Greenery, Seeds Not for Planting, Miscellaneous Processed Products) on 30 September 2022. The Plants for Planting Manual remains separate.
• Restricted and prohibited plants. APHIS lists categories that cannot simply be imported with a standard permit: federal noxious weeds and parasitic plants (research use only, in approved containment, under a PPQ 526 permit) and plants on the NAPPRA list, whose import is not authorized pending pest risk analysis (experimental use only, under a PPQ 588 permit).
• Federal Orders. APHIS can issue plant import Federal Orders, emergency measures that take effect immediately and can restrict or prohibit imports of a commodity or from a region. They sit outside the normal permit timeline, so check for a current order before relying on last year's conditions.

Because the permit and the certificate come from different governments, the US importer and the foreign exporter need to agree early on who is applying for which, and in what order. Questions about plant and plant product imports can be directed to APHIS at plantproducts.permits@usda.gov.

Paper, scans and ePhyto

An ePhyto is an electronic phytosanitary certificate exchanged directly between governments. The IPPC ePhyto Solution has two main parts: the Hub, a central system that passes certificates between NPPOs, and the Generic ePhyto National System (GeNS), a web-based system that lets countries without their own IT system issue, send and receive ePhytos through the Hub. In its March 2026 programme update, the IPPC reported 100 countries exchanging certificates live through the Hub, with a monthly average of roughly 250,000 to 300,000 certificates.

Two practical points follow from that:

• Do not assume an ePhyto will arrive. APHIS notes that a trading partner marked as able to send ePhytos may still choose not to send one for a given shipment, for example because of system limits or outages, so confirm with the exporter which form will arrive.
• A scan or emailed PDF is not an original. APHIS announced that from 1 October 2022 it no longer accepts "unoriginal" electronic phytosanitary certificates and forms. What it does accept is a certificate created through a participating country's ePhyto system, or a signed original paper form. If the certificate is neither, the cargo can stall at the port while a proper document is arranged.

If the paper original has to travel, build that into the plan: courier it to the broker or consignee, and do not assume a copy sent by email will clear the goods.

Inspection at the port of entry

In the US, US Customs and Border Protection handles the border and transfers live plant and propagative shipments to APHIS. APHIS operates 16 plant inspection stations at major ports (per its plant inspection stations page, last modified 24 August 2026), and most imported plant material intended for propagation must move through one to complete clearance. Inspectors review the permit and certificate and look at the material itself, using risk-based sampling. Once a shipment clears the station it is allowed to enter. If pests or disease are found, the station contacts the importer to discuss options.

For fresh produce, the same principle applies: the shipment is inspected, and the regulation (7 CFR 319.56-3) lets inspectors require cleaning or treatment of infested produce, refuse entry where the problem cannot be cleaned or treated or documentation is missing, and issue an emergency action notification.

What happens to non-compliant cargo

When a shipment fails, the outcome is usually one of three actions, directed by the inspector in writing:

1. Treatment, such as fumigation or another prescribed process, where a treatment exists that deals with the pest or contamination.
2. Re-export, shipping the goods back out of the country (or onward) at the importer's cost.
3. Destruction, where treatment is not possible or the commodity is prohibited.

In the US, this is formalised through an emergency action notification (PPQ Form 523), which sets a deadline for the importer to act. The costs of these outcomes are the importer's, and they do not stop while the decision is pending: storage, demurrage and detention continue to accrue. For how those charges work in US ports, see our guide to FMC demurrage and detention billing rules. Perishable cargo adds a second clock, because refrigerated produce does not wait. A treatment or hold of several days can destroy the value of a reefer load even if the paperwork is ultimately accepted.

Where this stops: wood packaging, food and other regimes

A phytosanitary certificate covers the cargo. Several neighbouring regimes cover other things, and mixing them up is a common source of delay:

• Wood packaging (pallets, crates, dunnage) is governed by ISPM 15 and proved by a stamp on the wood itself, not by a phytosanitary certificate for the shipment. See ISPM 15 wood packaging rules.
• Food entering the US also faces FDA prior notice and the Foreign Supplier Verification Program, which are separate from APHIS plant health. See FDA prior notice and FSVP. A shipment of fresh fruit can need both.
• Treatment or fumigation certificates issued by the treatment provider may be asked for in addition to, or inside, the phytosanitary process. Treat them as separate documents with their own requirements.

The full set of documents for a clearance, and who prepares each one, is laid out in our import documentation checklist.

What to do next

1. Identify the exact commodity (species, form and HS code) and the destination, then look up the importing country's current conditions before you quote or pack. For the US, search ACIR and check the permit pages and any Federal Order.
2. If a permit is needed, agree who applies for it, and start early: APHIS says a PPQ 587 application can take up to two months.
3. Ask the exporter to apply to the origin NPPO for inspection and the certificate, and check the draft details against the invoice, packing list and booking before it is issued.
4. Confirm whether the certificate will arrive as an ePhyto or as a signed paper original, and plan the courier if it is paper.
5. Choose a routing and arrival timetable that leaves room for inspection, especially for perishables, and make sure the broker knows what to expect at the plant inspection station.

If you need a forwarder or broker who handles agricultural cargo on your lane, more than 29,300 logistics companies are searchable by country and service in the CargoLinked directory, and the public requests board lists freight that shippers have posted for forwarders to quote on directly. For related calculations, see the freight tools.

This article is general information, current to 6 October 2026, and is not legal, customs or regulatory advice. Plant health rules change by commodity, origin and date, and a Federal Order or new import condition can apply at short notice. Confirm requirements with USDA APHIS, the importing country's plant protection authority or a licensed customs broker before you ship.