Indonesian Coffee Export to Japan: MHLW & JAS 2025 Guide

A practical, field-tested checklist to pass Japan’s MHLW pesticide limits for green coffee in 2025. How to find coffee MRLs in the Positive List, design a sampling plan that stands up to scrutiny, choose an ISO/IEC 17025 lab in Indonesia, select the right analyte panels (including glyphosate/glufosinate), and issue a COA your Japanese importer can use to avoid holds.

We’ve gone from shipments being randomly held in Tokyo Bay to 100% clean releases within a quarter by following a simple system. If you’re exporting Indonesian green coffee to Japan in 2025, this is the exact playbook we use.

The 3 pillars of clean entry into Japan

Know the MRLs you’re shipping against. Japan’s Food Sanitation Act uses the MHLW Positive List system. If a pesticide isn’t listed for coffee, the default MRL is 0.01 mg/kg. That’s unforgiving, especially for post‑harvest fumigants.
Test smart, not broad. Run a robust multi‑residue panel by GC‑MS/MS and LC‑MS/MS, then bolt on single‑analyte tests that multi‑res panels miss. Glyphosate and glufosinate are the classic misses. Fosetyl‑Al/phosphonic acid and ethephon can also be problematic, depending on farm practice.
Document like an importer. A clean Certificate of Analysis that aligns to the Positive List and your importer’s Import Notification workflow saves you days. We mirror how Japanese quarantine officers look at files. It’s saved us more than once.

Weeks 1–2: Map your risk and confirm MRLs

How do I find Japan’s MRLs for green coffee in the MHLW positive list?

Here’s the path we use in practice:

Start with the MHLW Positive List overview. It explains the default 0.01 mg/kg rule and links to resources. MHLW Positive List (English)
For the actual searchable MRLs, use the official database maintained with FAMIC. Search by pesticide name and commodity. Use “Coffee beans” as the commodity term. Japan MRL Search (FAMIC/MHLW)
If a pesticide isn’t listed for coffee beans, the default MRL is 0.01 mg/kg. Don’t assume “not listed” means “not checked.” It usually means “very low tolerance.”

Pro tip: Check both English and Japanese entries for ambiguous actives and synonyms. I’ve seen teams miss “hydrogen phosphide” when they only searched “phosphine.” The database uses Japanese commodity categories, so exact matching matters.

Do I need a separate glyphosate test for coffee beans going to Japan?

Yes. Most multi‑residue screens won’t cover glyphosate/glufosinate. Request LC‑MS/MS with derivatization or equivalent targeted methods for both. We typically add AMPA and 3‑MMPA if the lab offers them because importers sometimes ask for metabolite data. It’s a cheap insurance policy.

What about chlorpyrifos and other legacy actives?

Japan’s Positive List is strict on several organophosphates and phenylpyrazoles. We always include chlorpyrifos, profenofos, fipronil, and endosulfan in our review and ensure the lab’s LOQs are at or below 0.01 mg/kg for those. If your farming partners are fully organic, great. But we still test because drift and commingling happen.

Immediate takeaway for Weeks 1–2:

Build a farm‑level “allowed/prohibited” list mapped to Japan MRLs.
Confirm targeted add‑ons: glyphosate, glufosinate. Consider fosetyl‑Al/phosphonic acid and ethephon if relevant.
Pre‑season baseline test at least one lot per supplier so you’re not discovering surprises right before sailing.

Weeks 3–6: Sampling, testing and fumigation control

How much sample should I send and how should I composite it?

Our default for green coffee is 1.5–2.0 kg composite. Labs often need 200–400 g for analysis plus retention and repeats. Here’s the collection method that has held up under Japanese scrutiny:

Select increments from at least 20–30 bags across the lot. If you’re shipping 320 bags, we’ll sample every 10th bag as a rule of thumb.
Take 50–100 g per bag using a trier/probe that reaches midpoint, then composite into a clean food‑grade container.
Mix thoroughly. Split into: 1 kg to the lab, 500 g in sealed retention, and 300–500 g as a secondary retention in a separate seal.
Label with lot ID, bag count, harvest period, process type, and moisture. Chain‑of‑custody starts here. Keep it boring and very clear.

Which Indonesian labs are acceptable for Japan-bound pesticide testing?

Japan doesn’t formally “approve” foreign labs, but importers expect ISO/IEC 17025 accreditation with scope for pesticide residues in foods. Labs we’ve worked with or vetted in Indonesia include:

PT Saraswanti Indo Genetech (SIG), Bogor. Wide multi‑residue scope, glyphosate/glufosinate options.
SUCOFINDO laboratories, multiple sites. ISO/IEC 17025 scope includes pesticide residues.
SGS Indonesia, Intertek Indonesia, and Bureau Veritas Indonesia. All offer multi‑residue plus targeted add‑ons.
PT Angler BioChemLab, Surabaya/Jakarta. Strong LC‑MS/MS coverage.
PT Mutu Agung Lestari (MAL). Food residues scope.

Ask for: scope document, LOQs at 0.01 mg/kg for critical analytes, method references, uncertainty budgets and typical TAT. In our experience, the labs above can hit 7–10 business days for multi‑residue, 5–7 days extra for glyphosate/glufosinate.

Post-harvest fumigation residues: a quiet failure point

Phosphine (hydrogen phosphide) residues can trigger the 0.01 mg/kg default. If you fumigate with aluminum phosphide, build in an aeration schedule. We target at least 5–7 days degassing, with documented ventilation and temperature. If methyl bromide is used by a logistics provider for quarantine reasons, validate MRLs for bromide ion. Better yet, specify non‑MB treatments in your contracts.

Is ochratoxin A testing required in Japan?

MHLW hasn’t set a statutory OTA limit for coffee. But many Japanese buyers request OTA results aligned to EU guidelines. We treat OTA as “buyer optional, brand reputation essential.” It’s a cheap test and a useful quality signal.

Immediate takeaway for Weeks 3–6:

Send 1.5–2.0 kg composite samples to an ISO/IEC 17025 lab with 0.01 mg/kg LOQs.
Include glyphosate/glufosinate. Don’t rely solely on multi‑residue panels.
Control fumigation. Document aeration and avoid emergency MB treatments.

Weeks 7–12: Documentation that actually moves the shipment

What must be shown on the COA for MHLW and your importer?

Here’s the COA template that has prevented holds for us:

Product and lot identity. Coffee type, process, origin, lot ID, bag count, net weight, harvest period, moisture.
Matrix and methods. “Green coffee beans.” State GC‑MS/MS and LC‑MS/MS multi‑residue methods plus separate methods for glyphosate and glufosinate, with method references.
LOQs and units. LOQs at or below 0.01 mg/kg for key actives. All results in mg/kg. Explicitly state “<0.01 mg/kg ND” rather than “ND.”
Analyte list. Include a full appendix of covered analytes with LOQs. Japanese reviewers like seeing the scope, not just the hits.
Dates and chain‑of‑custody. Sampling date, receipt date, analysis dates. Unique CoC number.
Accreditation. Lab name, address, ISO/IEC 17025 number and scope code. Authorized signature with name and title.
Compliance statement. “Results comply with Japan MHLW Positive List for coffee beans based on search dated [YYYY‑MM‑DD].” Add database URL in a footnote.

Your importer will attach the COA to the Import Notification under the Food Sanitation Act when filing at a quarantine station before customs clearance. Provide it early, alongside a spec sheet and process description. This usually prevents a precautionary hold.

Avoiding inspection order status

If a country or product category repeatedly fails, MHLW can issue “inspection orders.” In practice, your individual exporter reputation matters. We maintain a shipment history log with COAs, sampling photos and fumigation records. After about 5–6 clean consignments, importers often reduce their own skip‑lot testing and trust your paperwork cycle.

Immediate takeaway for Weeks 7–12:

Issue a COA that mirrors MHLW reviewer logic.
Package your Import Notification binder for your buyer: COA, spec, fumigation/aeration record, farm declaration on pesticide use.
Maintain a clean history to avoid heightened inspection.

The 5 most common mistakes we see (and how to dodge them)

Running a multi‑residue panel without glyphosate/glufosinate. We see this 3 out of 5 times on first‑time exports. Add the targeted tests.
Sampling from 3–5 bags because “the lot is uniform.” Residues aren’t. Hit 20–30 bags minimum.
LOQs above 0.01 mg/kg for critical actives. If the LOQ is 0.02 mg/kg, it won’t help you. Ask the lab to meet 0.01 mg/kg.
Wrong commodity mapping in the MRL search. Always search “Coffee beans.” Don’t extrapolate from “beans” generically.
No fumigation aeration record. A single phosphine detect above 0.01 mg/kg is an avoidable failure. Plan the degassing window.

Quick answers to the questions we get most

What’s Japan’s default MRL if a pesticide isn’t listed for coffee? 0.01 mg/kg under the Positive List.
Do I need ochratoxin A? Not by law, but buyers often ask. We recommend running it.
Required sample size? Send 1.5–2.0 kg composite made from 20–30 bags with 50–100 g increments.
Accepted labs? Use ISO/IEC 17025 labs in Indonesia with proven pesticide residue scope. We’ve used SIG, Sucofindo, SGS, Intertek, BV, Angler BioChemLab and MAL.

Resources and next steps

Positive List overview: MHLW Positive List (English)
Search MRLs: Japan MRL Search (FAMIC/MHLW)

If you need a second set of eyes on your analyte list or COA format, feel free to Contact us on whatsapp. We’re happy to sanity‑check your plan before you book.

Looking for lots that consistently test clean? Our single‑origin supply is built around rigorous pre‑shipment testing. For buyers prioritizing low‑residue or organic programs, our Sumatra Arabica Organic Grade 2 Green Coffee Beans and Bali/Kintamani selections are frequent picks. You can browse current availability here: View our products.

One last thought. The regulation won’t get looser in 2025. But with a disciplined MRL lookup, the right lab panels and a COA that speaks your importer’s language, Japan can be one of the smoothest lanes you ship. We’ve seen it, shipment after shipment. And yes, it really can be that boring. That’s the goal.