A phytosanitary certificate is an official document, issued by the exporting country's plant protection authority, saying a consignment of plants or plant products was inspected and meets the importing country's plant health rules. If the destination requires one, you must have it before the cargo is accepted, so check the destination's requirements first and apply early.
Key takeaways
- Whether you need a certificate is decided by the importing country, not the airline, so check destination rules before you harvest or pack.
- In the US, you work with a state export certification specialist and an authorized certification official, and apply through PCIT.
- Inspection happens on the product you are shipping, so build certificate time into your schedule before the flight.
- ePhyto sends the certificate electronically between plant protection agencies; the IPPC reports 100 countries exchanging live, but confirm your destination accepts it.
- Re-exports of foreign-origin plant products need their own re-export certificate.
What is a phytosanitary certificate?
A phytosanitary certificate is an official plant health document that an importing country can require for plants and plant products, and it is issued by the exporting country, not by the airline or forwarder.
The International Plant Protection Convention (IPPC) sets the global standard in ISPM 12, "Phytosanitary certificates," which gives requirements and guidelines for preparing and issuing certificates for both export and re-export. Each country's national plant protection organization (NPPO) runs the certification system that applies the standard. APHIS, the US agency, describes the certificate as proof, required by importing countries, that plants and plant products meet their conditions.
For air freight this matters because perishables fly on tight schedules. A missing or incorrect certificate can hold cargo at the destination while fresh product loses shelf life. Our perishables air freight guide covers the wider handling picture; this article focuses on the paperwork.
Which air freight shipments need one?
The importing country decides, so the answer depends on the commodity, the destination and sometimes the variety or origin.
Typical candidates are fresh fruit and vegetables, cut flowers, live plants, cuttings, seeds and some processed plant products. Some products are not eligible for certification at all: APHIS publishes a list of commodities it cannot certify, and importing countries may ban or restrict certain products outright. In the US, the destination's conditions are looked up in APHIS's Phytosanitary Export Database (PExD). Outside the US, ask your NPPO.
If you are unsure, do not guess. APHIS advises contacting an export certification specialist when you cannot tell whether a certificate is needed, and the same logic applies anywhere: ask the authority before you ship, not after the cargo is booked. Related guides: exporting fresh fruit and vegetables by air and how cut flowers are flown to market.
How do you get a phytosanitary certificate?
You contact your plant health authority, arrange an inspection and apply, and the certificate is issued once the product passes.
The US process, as APHIS describes it, has three main steps:
- Contact your state's export certification specialist. APHIS has specialists nationwide who can explain the requirements for a given destination.
- Work with an authorized certification official (ACO). The ACO arranges the required inspections and helps you apply through the Phytosanitary Certificate Issuance and Tracking System (PCIT).
- Receive the certificate. Once issued, it is available online right away to print. If you cannot print it, you can ask for mail, courier or in-person pickup in a comment on your application.
User fees apply and vary depending on which federal, state or county authority inspects and issues the certificate. Other countries run their own systems and fees, so confirm the process with your NPPO.
When should you apply for the certificate?
As early as the process allows, because inspection is done on the actual consignment and the certificate cannot be finished before the product is ready.
APHIS does not publish a standard processing time, so ask your ACO or specialist how far ahead to book an inspection for your commodity and season. Build the certificate into your packing and tender plan: product ready, inspected, certificate issued, then trucking to the airport and the flight. Some importing countries insist the certificate be issued before the shipment leaves, so plan for that rather than hoping to send it after departure.
Also check that the details on the certificate match the rest of the file. Consignee name, product description, quantity and origin should agree with the commercial invoice and the air waybill. A mismatch is an easy way to create a delay at import inspection.
What is an ePhyto and does it replace the paper certificate?
An ePhyto is the electronic equivalent of a paper certificate, so it replaces paper only where both countries have agreed to exchange it.
The IPPC describes an ePhyto as an electronic phytosanitary certificate in XML format that carries the same information as the paper version and follows ISPM 12. The IPPC ePhyto Solution has three parts: a central server, the Hub, that transfers ePhytos between NPPOs; the Generic ePhyto National System (GeNS), a web-based system for countries without their own electronic system; and a common format with standardized codes and lists.
Adoption is growing. In its March 2026 programme update, the IPPC reported a milestone of 100 countries exchanging phytosanitary certificates live through the Hub, along with a 20 percent rise in average monthly exchange volumes. That is not every country, so check with your NPPO or the importing country's agency whether ePhyto is accepted for your destination and commodity. Where it is not, you still need the paper certificate, and some importers may ask for a copy to travel with the cargo.
What if the goods are re-exported?
Foreign-origin plant products that you ship onward need a separate re-export certificate, not the original certificate alone.
APHIS explains that a re-export certificate covers plants or plant products that entered the US with a valid phytosanitary certificate. It certifies that the product still meets the importing country's current rules, based on the original certificate, an additional inspection, or both, and that it was not exposed to infestation risk in storage. ISPM 12 also covers re-export certificates, so the same principle applies in other countries, with details set by each NPPO.
How does the certificate fit with other air freight paperwork?
It is one document in a set, and the requirements differ by lane.
| Document | What it does | Who provides it |
|---|---|---|
| Phytosanitary certificate | Shows plant health conditions of the importing country are met | Exporting country's plant protection authority |
| Commercial invoice | Describes goods and value for customs | Shipper |
| Air waybill | Contract of carriage and shipment record | Airline or forwarder, from shipper data |
| Other permits (food safety, import permits) | Destination-specific conditions | Varies by destination authority |
Ask your forwarder to review the full set before the cargo is tendered. Jumbo Air Cargo's JumboFresh service handles perishable air freight, and the chargeable weight calculator helps you estimate billable weight for packed produce or flowers. Which documents the destination requires remains something to confirm with its authority.
What are the most common mistakes?
Most problems come from timing and mismatches rather than the certificate itself.
- Not checking destination rules first. Requirements are set by the importing country and change, so do not copy last season's file.
- Applying too late. Inspection must happen on the finished consignment.
- Details that do not match. The certificate, invoice and waybill should tell the same story.
- Assuming ePhyto is accepted everywhere. Confirm it for your destination and commodity.
- Forgetting re-export rules. Foreign-origin goods need their own certificate.
Treat the NPPO and the importing country's agency as the final word. This article is general guidance, not a substitute for the official requirements for your commodity and lane.
Frequently asked questions
What is a phytosanitary certificate?
It is an official document that tells the importing country a plant or plant product consignment meets its plant health conditions. The IPPC sets the international standard for these certificates in ISPM 12.
Who issues a phytosanitary certificate?
The exporting country's national plant protection organization or its authorized officials. In the United States, USDA APHIS works with state and local authorized certification officials who inspect the product and process the application.
What is an ePhyto?
An ePhyto is the electronic equivalent of a paper phytosanitary certificate, in XML format, carrying the same information. It travels between national plant protection organizations through the IPPC ePhyto Hub.
Does a certificate replace other export paperwork?
No. It is one document in the file. You still need the commercial invoice, air waybill and any customs, food safety or other permits the destination requires.
