Indonesian Coffee Export to Japan: JAS & FSA 2025 Guide

A practical, exporter-focused checklist for passing Japan’s Food Sanitation Act (FSA) on green coffee in 2025. What to test, how to spec the lab, sampling that holds up at quarantine, and the exact documents your importer needs for NACCS.

If you’re exporting Indonesian green coffee to Japan in 2025, your real gatekeeper isn’t customs. It’s the Food Sanitation Act. We’ve seen pristine coffees held for days because a lab report didn’t list LOQs, or a pesticide exceeded Japan’s positive-list default of 0.01 ppm. The good news. With the right pre-shipment routine, you can turn FSA from a risk into a repeatable checklist your buyers trust.

Quick note on “JAS vs FSA.” JAS is a labeling standard. If you’re not selling as organic or using JAS marks, you don’t need JAS certification to import green coffee. Your immediate priority is FSA compliance.

The 3 pillars of smooth FSA clearance

Test against Japan’s positive list. The MHLW sets pesticide Maximum Residue Limits (MRLs). If there’s no specific MRL for coffee, the default is 0.01 ppm. That “default 0.01 ppm” trips up more exporters than anything else. We always confirm target analytes and MRLs in the MHLW database before sampling.
Use the right lab, methods and LOQs. Your COA must be believable to a quarantine officer. That means an ISO/IEC 17025 accredited lab, LC-MS/MS + GC-MS/MS multi-residue screens, and LOQs at or below the strictest MRLs. If any analyte on your panel has an LOQ above the MRL, you’re exposed.
Paperwork that matches NACCS. Your importer files the FSA Import Notification through NACCS. If your COA doesn’t map to the lot definitions, bag counts and marks on the invoice and packing list, expect questions or a hold.

What FSA tests are actually required for green coffee?

Japan applies the Food Sanitation Act positive list system for pesticides. In practice we recommend:

Multi-residue pesticides. A 500–700 compound screen covering organophosphates, pyrethroids, neonicotinoids, carbamates, triazoles and others by LC-MS/MS and GC-MS/MS. LOQs should be 0.005–0.01 ppm for most analytes.
Ochratoxin A (OTA). There isn’t a specific MHLW compositional standard for OTA in green coffee as of Q3 2025, but buyers and quarantine stations may still request results in risk-based checks. We run OTA by LC-MS/MS or HPLC-FLD with an LOQ at 1 µg/kg or lower. It’s inexpensive insurance.

When do we add more? If the buyer’s spec includes mycotoxins beyond OTA, or if the country/commodity has a recent violation pattern, we add aflatoxins and glyphosate/AMPA. Check the latest MHLW updates because MRL revisions are frequent.

Do I need to test every lot or can I use periodic testing?

Our rule of thumb. Test every export lot to Japan until you’ve built a clean track record with that buyer and product. Japan uses risk-based inspection. If your HS 0901 coffee from Indonesia starts showing violations, the Quarantine Station can increase inspection frequency and require on-arrival testing. Periodic testing is only realistic once the importer’s compliance team is comfortable and there’s no monitoring instruction in place for your item.

Which pesticides most often trigger positive-list violations in Indonesian coffee?

Patterns we’ve seen:

Chlorpyrifos and chlorpyrifos-methyl. Often sit at or just above the 0.01 ppm default if used upstream. We treat them as zero-tolerance and verify ND.
Lambda-cyhalothrin, cypermethrin, deltamethrin. Pyrethroids can linger on cherry skin. Poor post-harvest handling raises risk.
Carbaryl and carbofuran. Legacy use can appear in mixed smallholder lots.
Profenofos, endosulfan residues in older stock. Rare now, but they still pop up in past-crop blends.

Practical tip. If you buy from multiple kecamatan or collectors, segregate supply and test composites by source. One hot pocket can contaminate a large blend.

Does Japan require Ochratoxin A testing for green coffee beans?

Not as a universal legal limit in green coffee. But importers frequently add OTA to the spec, and Quarantine Stations can request it based on risk. We include OTA by default for Japan-bound shipments. It’s a low-cost way to avoid a preventable hold.

Sampling that holds up under scrutiny

Labs don’t fail shipments. Sampling does. Here’s a protocol that works.

Lot definition. Fix your lot at max 19.2 tons per COA if possible. Larger lots increase variability and re-test cost.
Sample size. Send 1–2 kg of green beans to the lab. In-house, draw primary samples from at least 10 bags across the lot. If you have 320 bags, sample every 30–40 bags in a staggered pattern.
Composite method. Combine equal weights from each primary pick to form a 1–2 kg composite. Mix thoroughly. Grind a sub-sample to a homogeneous powder before analysis. We never test whole beans.
Chain of custody. Label bag marks, lot code, bag count, harvest year, processing and moisture. Include photos of lot labels. We add a simple sampling form with signatures from QC and warehouse.

This is the fastest way to defend your COA if the Quarantine Station asks how the sample represents the lot.

Lab specs that pass quarantine questions

Accreditation. ISO/IEC 17025. Verify the lab’s accreditation scope includes pesticide residue in plant/coffee matrices.
Methods. LC-MS/MS and GC-MS/MS multi-residue. Ask for the analyte list. For Japan, we target a broad 500–700 compound panel.
LOQs vs MRLs. LOQs at or below the strictest MRL. If Japan uses 0.01 ppm default, we specify LOQ 0.005–0.01 ppm. Results should show “ND < LOQ” explicitly.
Turnaround. 5–7 working days for pesticides, 2–3 for OTA. Budget buffer time before vessel cut-off.
Trusted options we’ve used. International networks like SGS, Intertek and Eurofins. In Indonesia, ISO 17025 labs such as Sucofindo, Saraswanti and Mutu can run coffee pesticide panels. Always confirm current scope.

How to format your COA and documents for NACCS

Your importer will submit the FSA Import Notification via NACCS. We provide a clean package:

COA. On lab letterhead, with sample ID, lot code, origin, product name “Coffee beans, green,” matrix “plant product,” methods, analyte list with results and LOQs, date, and an authorized signature/stamp. If space is limited, include a full analyte list as an annex.
Invoice and packing list. Match descriptions, lot code, bag count, marks and weights to the COA.
Process flow. A one-page flow from cherry reception to dry mill and bagging. Include processing type (washed, semi-washed, natural), drying, hulling, sorting and final moisture.
Photos. Bag marks and palletization. Optional but speeds questions.

Need a COA template that quarantine officers don’t push back on. If you’d like our template and sampling form, just contact us on whatsapp.

What documents should I provide my importer for the FSA import notification?

At minimum:

Commercial invoice, packing list and B/L or AWB.
COA for pesticides. OTA COA if requested by the buyer.
Process flow and product spec sheet. 100% coffee beans. No additives.
Harvest year and lot code mapping to the COA.

We also share farm or cooperative declarations when available. It’s not a legal requirement, but it helps compliance teams.

Timeline we use for Japan-bound shipments

T-21 to T-18 days. Draw samples. Run pesticide multi-residue and OTA.
T-14 days. Receive COAs. Cross-check LOQs vs MRLs. Re-sample if anything is marginal.
T-10 days. Finalize documents. Align invoice, packing list and COA identifiers.
On arrival. If flagged for inspection, expect a hold of 3–7 working days for pesticides, sometimes up to 10. Having a credible pre-shipment COA often shortens the review. If the Quarantine Station samples, cooperate quickly on any questions about lot definition and sampling.

Roasted vs green coffee. Should I test differently?

We test green coffee pre-shipment. It’s the most conservative and widely accepted. If you export roasted coffee, FSA still applies and importers may accept either a green bean COA for the source lot or a roasted-bean COA. Clarify early with the buyer’s QA team. We’ve found roasted COAs are appreciated for private-label retail, but green-bean COAs remain the baseline.

The 5 mistakes that get coffee held in Japan

LOQs above the MRL. A result of “<0.05 ppm” means nothing if the default MRL is 0.01 ppm.
Incomplete analyte list. A 250-compound screen that misses a common pyrethroid is risky.
Poor sampling. Testing four bags of a 300-bag lot won’t hold up. Composite properly.
COA-invoice mismatch. Different lot codes or bag counts invite questions.
Assuming OTA isn’t needed. It’s not always mandatory, but it’s an easy request from buyers and regulators. Include it.

Helpful resources and next steps

Japan MHLW MRL search. Use the MHLW database to check “coffee beans/0901” for current MRLs and defaults. Recheck before every shipment. MRLs shift more than most people realize.
NACCS. Align with your importer’s NACCS workflow. They submit the Food Sanitation Act import notification with your COAs and docs attached.

If you want Indonesian lots that align with Japan’s quality expectations, we can prep pre-shipment COAs on request for single-origin options like Arabica Bali Kintamani Grade 1 Green Coffee Beans, Blue Batak Green Coffee Beans and Arabica Java Ijen Grade 1 Green Coffee Beans. You can also browse the full range and shortlist SKUs suited to your blends. View our products.

In our experience, three things separate shipments that glide through from those that stall. A lab with the right scope and LOQs. Sampling that reflects the lot. And documents that line up perfectly in NACCS. Nail those, and Japan becomes one of the most predictable lanes you’ll ship all year.