An exporter-first, step-by-step playbook to secure and upload the FSSAI health certificate for fish and fishery products from Indonesia to India—what it must say, who issues it, which tests to reference, and how to avoid the rejections we see most often at Indian ports.
Hook
We’ve gone from first-time shipments getting held up for 7–10 days to routine green-channel clears in under 48 hours by following one exact system for the FSSAI health certificate. This guide is that system. If you’re exporting Indonesian seafood to India in 2026, use this to brief your team, your lab, and your CHA. You’ll save days and real money.
The 3 pillars of fast import clearance
Here’s the thing. The FSSAI health certificate is simple on paper, but most delays come from tiny mismatches across documents. We’ve found three pillars keep shipments moving:
-
Correct issuer and certificate format. Use the FSSAI “Model Health Certificate for Fish and Fishery Products” and get it issued by Indonesia’s competent authority for fish. That’s BKIPM (Badan Karantina Ikan, Pengendalian Mutu dan Keamanan Hasil Perikanan). Not Barantan. Barantan handles agriculture. Fish and fishery products are BKIPM’s lane.
-
Attestations and tests aligned to product risk. Shrimp needs antibiotic residue language. Tuna and other scombroids need histamine. Some ports also look for Vibrio statements on raw ready-to-cook products. Your certificate and attached CoA should anticipate this. We’ll spell it out below.
-
Clean digital trail in FICS. The data in FICS must mirror the physical certificate, invoice, packing list, and B/L. Container numbers, species names, net weights, pack counts, dates, seal numbers. If one line is off, you invite sampling, re-upload requests, or rejection.
Practical takeaway: Build a single source of truth spreadsheet for each shipment, then derive every document from it. No manual retyping.
Week 1–2: Market research and validation (for your paperwork)
You might be thinking, paperwork isn’t “market research.” In our experience, it is. You validate your clearance pathway before you book space.
-
Confirm if the product is human consumption fish/fishery product. If yes, the FSSAI health certificate is mandatory. We’re asked a lot: Is a health certificate mandatory for frozen shrimp imports into India? Yes. It’s required for shrimp and for fish/fishery products across the board since the FSSAI order that took full effect in late 2023 and continues through 2026.
-
Decide the species and cut. Then pre-map test requirements. Examples:
- Shrimp like our Frozen Shrimp (Black Tiger, Vannamei & Wild Caught) often trigger antibiotic residue scrutiny. Plan a CoA covering chloramphenicol and nitrofuran metabolites at minimum, plus a representative screen for other classes (tetracyclines, sulfonamides, quinolones) based on your farm/source risk.
- Scombroid-forming species like Yellowfin Saku (Sushi Grade), Yellowfin Steak, Mahi Mahi Fillet, or Wahoo Portion (IQF / IVP / IWP) should include histamine results and a time–temperature control statement. Non-scombroids like Grouper Fillet (IQF) or Red Snapper Portion (WGGS / Fillet) don’t usually need histamine.
-
Check if you’re shipping anything that falls outside FSSAI’s fish-for-human-consumption lane. Dried fish for human consumption still needs the FSSAI health certificate. Fish meal or feed may fall under DAHD/AQCS permits, not FSSAI. Different path. Don’t mix them in one B/L.
Practical takeaway: Lock your product risk profile, then lock your test list with your lab and BKIPM officer early.
Week 3–6: MVP creation and testing (drafting, lab, and BKIPM)
This is where most teams lose time. Build a working “MVP” set of documents and test it internally before you send anything to print.
-
Who issues the certificate? BKIPM. They issue the pre-shipment health certificate aligned to FSSAI’s model format. We prepare a draft for BKIPM review, matched to our invoice and packing data. The best practice is to pre-share species, scientific names, HS codes, lot numbers, pack counts, container and seal numbers.
-
What exactly should the certificate say? The FSSAI model health certificate includes identity of consignor/consignee, country of origin, processing/packing establishment approval number, description of fish/fishery product with scientific name, lot/batch, quantity, production and expiry dates, container and seal numbers, and health attestations that the products were produced in approved facilities under official control and comply with FSSAI standards. We add an annex if there are multiple species or many lots.
-
What tests should be mentioned? Two layers usually work best.
- In-certificate attestations that the products conform to FSSAI regulations with respect to contaminants, microbiological criteria, residues, and additives.
- A separate lab CoA attached. For shrimp, we typically include chloramphenicol and nitrofuran metabolites (AOZ, AMOZ, AHD, SEM) with LOQ at or below Indian tolerance, plus a multi-residue screen as needed. For scombroids, histamine results on a representative sample. For raw fishery products, some ports ask for Vibrio screening language. Heavy metals may be requested for larger pelagics.
-
FSSAI fish health certificate vs sanitary import permit. Do I also need a sanitary import permit? For fish and fishery products for human consumption, the FSSAI health certificate plus FICS clearance is the path. SIP is typically for certain livestock products and feeds via DAHD, not your standard frozen fillets or shrimp for human consumption.
-
Dates and validity. Issue the health certificate on or just before the shipment date. We’ve seen rejections when the certificate date is later than the on-board date or when production dates don’t match pack labels. Keep the chain consistent.
-
One certificate per shipment or per container? FSSAI wants one certificate per consignment. Practically, if you have multiple containers under one B/L and one invoice, you can cover them under one certificate that lists each container and seal number. If containers sail on different vessels or dates, or hold different product risk profiles, we recommend separate certificates. It reduces “partial hold” headaches.
Practical takeaway: Build your certificate draft and CoA as a kit. Keep annexes tidy and mirror all numbers against the invoice, packing list, and B/L.
Week 7–12: Scale and optimize (FICS and port playbook)
Once you’ve got the kit, you scale by cleaning up your digital trail.
-
FICS upload path. Your importer or CHA files the FSSAI online application in FICS and uploads the health certificate, CoA, invoice, packing list, B/L, and label images. The product category must match fish and fishery products. Data must mirror the certificate exactly. Use your single source of truth spreadsheet to populate FICS.
-
Are scanned or digitally signed certificates accepted? Ports do accept digitally signed BKIPM certificates with secure QR or web verification, and scanned copies for pre-scrutiny. But the original often still travels with the document set. Our rule: upload the digital copy in FICS and make sure the original or a verifiable digital original is available at inspection.
-
Minor mistakes at clearance. Can they be corrected? Don’t rely on it. FSSAI officers typically won’t accept hand-corrected or overwritten fields. If there’s a typo in species name, container number, or dates, ask BKIPM to reissue or issue a countersigned corrigendum, then re-upload in FICS. You may avoid detention if your CHA flags the correction proactively.
-
Random sampling. Even with a perfect file, sampling happens. If it’s histamine risk species, your timeline depends on lab turnaround. We plan for 2–5 working days. Building a track record of compliance helps reduce surprise checks over time.
Need help mapping your product to the right attestation wording or test list? If you want a second set of eyes before you sail, Contact us on whatsapp. We can share a redacted sample pack.
5 biggest mistakes that sink seafood clearance
We see the same issues over and over. Avoid these and you’ll be ahead of the pack.
-
Using the wrong competent authority. Barantan instead of BKIPM. India will reject it. BKIPM must sign fish and fishery products from Indonesia.
-
Certificate date after on-board date. This is low-effort to fix before sailing and high-impact if you miss it. Align the sign-off date with your ETD.
-
Inconsistent container and seal numbers across certificate, invoice, and FICS. One digit off can trigger holds. Cross-check.
-
Missing risk-aligned tests. Shrimp without nitrofuran/chloramphenicol results, or tuna without histamine. Your shipment becomes the lab’s teaching case.
-
Overloaded certificate text but no readable annex. Cramming 12 lots, three species, and five pack sizes into a tiny table invites transcription errors. Use a clean annex, reference it clearly, and keep font legible.
Practical takeaway: A 15-minute internal document reconciliation before you courier originals typically saves 3–5 days at port.
People ask us these exact questions
Who is the competent authority in Indonesia that can issue the seafood health certificate for India?
BKIPM, the Fish Quarantine and Quality Control Agency under the Ministry of Marine Affairs and Fisheries. They issue the pre-shipment health certificate in line with FSSAI’s model.
What tests should be mentioned on the certificate for shrimp or fish fillets?
At minimum, include the FSSAI compliance attestation in the certificate and attach a lab CoA. For shrimp: chloramphenicol and nitrofuran metabolites, plus an appropriate multi-residue panel. For scombroids: histamine. For raw fishery products likely to be cooked: we often include Vibrio language if the port historically expects it.
Does each container need its own health certificate?
Not necessarily. One certificate per consignment can cover multiple containers under one B/L and invoice. If sail dates or products differ, we recommend separate certificates to de-risk.
Will FSSAI accept scanned or digitally signed health certificates at the port?
Yes, for pre-scrutiny and often for final if the digital signature is verifiable. Many officers still ask to see the original or a secure digital original. Plan to provide it.
Can minor mistakes on the certificate be corrected during clearance?
Only via reissue or an official correction by BKIPM. Handwritten edits are almost never accepted. Upload the corrected version in FICS.
Do I also need a sanitary import permit?
For fish and fishery products for human consumption, generally no. The FSSAI health certificate and FICS clearance pathway applies. Live aquatic animals, feed, and non-food uses may require other permits under DAHD/AQCS.
Resources and next steps
- Want examples of well-specified products that consistently clear? See our India-ready lines like Grouper Fillet (IQF), Red Snapper Portion (WGGS / Fillet), and Frozen Shrimp (Black Tiger, Vannamei & Wild Caught). Their specs map cleanly to FSSAI requirements. If you’re planning tuna or mahi shipments, pair them with histamine controls like our Yellowfin Saku (Sushi Grade) program.
- Lining up a Q2 or Diwali-season import window? Build your certificate draft, annex, and CoA now and validate the wording with your CHA and BKIPM officer before you book reefer space. Then mirror everything into FICS from a single source of truth.
If you want us to review your draft certificate or map tests to your exact species and cut, just View our products and tell us which SKUs you’re targeting. We’ll share the sample wording we use and what’s worked at Nhava Sheva, Chennai, and Mundra recently.
Here’s the reality. FSSAI’s model health certificate looks like a one-page checkbox. But when it precisely matches your product risk and your digital trail, clearance becomes repeatable. Do that a few times and the process stops being a fire drill and starts being a calendar reminder.