Yes, if your shipment is a plant, a plant product, an animal-origin product, or contains CITES-listed species material. This clearance is separate from Japan Customs (税関) release and from any Ministry of Health, Labour and Welfare (厚生労働省) food notification. It is administered by the Ministry of Agriculture, Forestry and Fisheries (農林水産省, MAFF), and a shipment can pass customs review and still be held, or refused entry, if it fails this separate check.
Is Plant and Animal Quarantine the Same Review as Customs Clearance?
No. Customs clearance and quarantine clearance are two distinct legal reviews run by two different ministries, and satisfying one does not satisfy the other. Japan Customs assesses tariff classification, valuation, and declaration accuracy under the Customs Act; MAFF assesses biosecurity risk in the commodity itself, regardless of what the customs entry says about it.
In practice this means the paperwork sequence has two independent gates, not one combined gate. A shipment can be correctly classified, correctly valued, and fully compliant on the customs side, and still sit at the port pending or failing quarantine inspection. The two clearances are commonly bundled together in a client's head as "getting the cargo through," and that is exactly where shipments get stuck: nobody separately confirmed the plant or animal-origin content actually cleared MAFF's own inspection.
Which Imports Require MAFF Quarantine Clearance?
Three categories trigger a MAFF quarantine step: plants and plant products, animal-origin products, and any material from a CITES-listed (Convention on International Trade in Endangered Species) species. Each category sits under its own statute and its own inspection body inside MAFF, so a shipment touching more than one category (a leather-and-wood gift item, for example) can face more than one quarantine review at once.
Plants and plant products are inspected by MAFF's Plant Protection Station under the Plant Protection Act (植物防疫法). Animal-origin products, live animals, and related material are inspected by MAFF's Animal Quarantine Service under the Act on Prevention of Infectious Diseases in Domestic Animals (家畜伝染病予防法), which also carries Japan's rabies-prevention framework for the species it covers. Products containing CITES-listed species material, such as certain wood species, exotic leather or skins, or ivory, fall under Japan's domestic implementation of CITES, the Act on Conservation of Endangered Species (種の保存法). None of these three reviews is optional based on the customs entry alone; each is triggered by what the commodity physically is. If your product falls into the medical device, food, or cosmetics categories layered on top of a plant or animal-origin base, the PSE, PSC and food safety compliance framework runs as a parallel MHLW track, not a substitute for the MAFF review.
What Does the Plant Quarantine Process Under the Plant Protection Act Require?
A plant quarantine inspection at the port of entry is required for plant and plant-product imports under the Plant Protection Act (植物防疫法), and the standard supporting document is a Phytosanitary Certificate issued by the exporting country's own plant protection authority. Without that certificate presented at the Plant Protection Station, the commodity has no standing basis for the inspection to proceed on the exporter's declared pest-and-disease status.
The certificate is issued in the country of origin, before the shipment leaves, which means it cannot be obtained retroactively once cargo has landed in Japan. A shipment arriving without one, or with a certificate that does not match the actual commodity, faces the same practical outcome as failing the inspection outright: the goods do not move past the Plant Protection Station regardless of what the customs declaration says. Any importer sourcing raw agricultural commodities, cut flowers, seeds, wood, or unprocessed plant material should confirm the exporting country's phytosanitary certification process before booking the shipment, not after it arrives.
What Does Animal Quarantine Require, and Why Does It Vary by Product and Country?
Animal-origin product requirements are set by MAFF's Animal Quarantine Service under the Act on Prevention of Infectious Diseases in Domestic Animals (家畜伝染病予防法) and the associated rabies-prevention framework, and they differ by species, product type, and country of origin. There is no single uniform animal-import rule, because the requirement tracks the exporting country's disease status for that specific species and product, not a general Japan-wide standard.
This is the category most often mishandled precisely because a client assumes one clearance covers "animal products" generically. A raw hide from one country of origin and a processed leather good from another can face entirely different documentary requirements, even where both eventually reach the same tariff line at customs. Anyone importing pet products, animal-derived materials, or livestock-adjacent commodities should confirm the specific requirement for their product's exact country of origin before shipping; the IOR structure for pet products and animal-derived goods addresses the importer-of-record side of this category, but it does not substitute for confirming the underlying quarantine requirement itself.
When Do You Need a CITES Import Permit?
You need a CITES import permit whenever your product contains material from a species listed under the Convention on International Trade in Endangered Species, which Japan implements domestically through the Act on Conservation of Endangered Species (種の保存法). Common trigger materials include certain wood species, exotic leather or skins, and ivory, though the full list of covered species and products is far broader than these examples.
CITES-listed species are classified into Appendix I, II, or III, and which Appendix a given species sits in determines the permit process that applies. This post does not state which specific commodities fall into which Appendix, because that classification is species-specific and changes over time; confirm the classification for your exact product against MAFF's own published guidance before assuming a permit is or is not required. Getting this wrong is not a minor paperwork gap: importing Appendix-listed material without the correct permit is a customs-enforcement matter in addition to a MAFF one.
Key points:
(a) Quarantine clearance (MAFF) and customs clearance (Japan Customs) are independent legal reviews; passing one does not satisfy the other, and a shipment can be held or refused entry on the quarantine side alone.
(b) Plant and plant-product imports need a Plant Protection Station inspection under the Plant Protection Act (植物防疫法), normally supported by a Phytosanitary Certificate obtained in the country of origin before shipment.
(c) Animal-origin products and CITES-listed species material each carry their own permit logic, respectively under the Act on Prevention of Infectious Diseases in Domestic Animals (家畜伝染病予防法) and the Act on Conservation of Endangered Species (種の保存法) with its Appendix I/II/III structure, and both require confirming the specific requirement per product and origin rather than assuming a general rule applies.
Frequently Asked Questions
If my shipment already cleared Japan Customs, does that mean quarantine is done too?
No. Customs clearance and MAFF quarantine clearance are separate reviews run by different ministries, and a customs release does not confirm the quarantine inspection passed. For plant, animal-origin, or CITES-covered cargo, confirm the quarantine result independently rather than treating a customs release as proof the shipment is fully cleared.
Do I need a Phytosanitary Certificate for every plant-based product, or only raw agricultural goods?
The Plant Protection Act (植物防疫法) inspection applies to plant and plant-product imports generally, and a Phytosanitary Certificate from the exporting country's plant protection authority is the standard supporting document presented at import. Whether your specific product requires one depends on what it physically is; confirm with the Plant Protection Station or a coordinating provider before shipping rather than assuming a processed product is exempt.
How do I find out if my product's country of origin has an approved animal quarantine pathway to Japan?
Animal quarantine requirements under the Act on Prevention of Infectious Diseases in Domestic Animals (家畜伝染病予防法) are set per species, product type, and country of origin, tracking that country's disease status, so there is no single answer that applies across countries. Confirm the specific requirement for your product and its exact country of origin with MAFF's Animal Quarantine Service, or through a provider coordinating the customs and regulatory filing package, before booking the shipment.
Conclusion
Plant, animal-origin, and CITES-covered imports into Japan carry a quarantine step that sits alongside customs clearance and, for retail food, alongside MHLW notification, and each of these three reviews has its own failure mode independent of the others. Confirming the applicable MAFF pathway, the correct supporting certificate, and the correct permit classification before the shipment leaves origin avoids a hold that customs clearance alone cannot resolve. Buyers evaluating medical device import routes or any other regulated product category should apply the same discipline: identify every ministry with a claim on the shipment, not just the one that issues the final release.
This article is informational only and does not constitute legal, tax, or regulatory advice. Consult a qualified advisor before acting on the content. Last updated: August 2026.