Find out the exact reasons customs puts shipments on hold, from missing PODs and wrong HS codes to quarantine holds, and the practical steps logistics teams use to prevent delays and penalties.
When a customs flag becomes a business problem
A customs hold can stop a container, accumulate storage fees, and disrupt delivery SLAs in hours. Luckily, most holds are not that severe- they’re preventable. Such as paperwork errors, classification errors, proof of delivery documents missing or ag paperwork is missing. The way you document, classify, and pre-declare the shipment will dictate if customs clears the shipment in a few hours or keeps it in uncertainty.
Top Reasons Cargo Gets Flagged, and Exactly What to Fix
1) Incomplete or incorrect documentation
The number one reason for a hold is due to missing or inconsistent Commercial Invoices, Bills of Lading, or Packing Lists. Customs uses these documents to verify the transaction value, the consignees, and commodity description – all of these will trigger a hold so a newbie can review! Solution: develop a set template, automate fields validation, and require Broker sign off before the vessel load/air departure.
2) Wrong or vague HS (commodity) codes
Using an incorrect HS/HTS code can not only slow down the clearance process but may also put you at risk of back-duties and fines, or seizure if the incorrect classification resulted in under-payment. Binding rulings, automated classification tools, and dual verification (photo of the product + specification sheet) should be used on high-risk SKUs.
3) Value or origin discrepancies (price, Incoterms, country-of-origin)
Customs evaluates the values you declare against reasonable market expectations. If the customs agent questions your value as being too low or origin markings don’t align (e.g., invoice shows incorrect COO on invoice vs. BL), you may be subjected to a statistical review or targeted validation hold. Make sure to keep your invoices consistent, and remember to submit the supporting purchase orders and proof of transaction as needed.
Read more: Top 5 Load Tendering Mistakes in Freight Operations + Avoid Them
4) Missing or inadequate Proof of Delivery (POD)
For certain release processes and bonded movements, customs or the consignee will ask for PODs to close the transaction. Electronic PODs (signed e-PODs or timestamped photo PODs) reduce disputes and speed post-release reconciliation. Ensure your POD format includes recipient name, signature/photo, timestamp, and reference numbers.
5) Agricultural / quarantine holds and prohibited goods
Food, plants and animal products are often detained/held even for phytosanitary and/or quarantine inspections. The importer must provide appropriate certificates and comply with APHIS/plant quarantine policy. If they do not, cargo can be refused, destroy and/or can require treatment (at the cost of the importer.) For agricultural products, pre-clearance and the appropriate COEs for clearance process should be strictly adhered to.
6) Security, sanctions, and targeted inspections
In order to identify which shipments should be examined further Customs utilizes automated risk profiling methods (e.g. controlled goods & destinations, unusual routing, etc.). High-value or unusual movements are run through a higher level of scrutiny regardless of the tripARTICATE robustness of an AEO Demonstrate a continuous and transparent declaration to the broker (e.g. chain of custody).
Quick Customs Checklist: What to Do Today
| Action | Why it stops holds |
| Use a validated Commercial Invoice template (auto-fields) | Eliminates mis-typed values, missing consignee fields and inconsistent Incoterms |
| Pre-classify SKUs and get binding rulings for high-value products | Prevents HS disputes and duty reassessments |
| Collect e-POD (photo + signature) and store in shipment file | Provides immediate delivery proof for customs or clients |
| Confirm phytosanitary & quarantine certificates before booking | Avoids treatment or destruction at arrival |
| Pre-file manifest / ISF / e-manifest before arrival | Gives customs time to validate and reduces risk of “arrival hold” |
PODs, HS Codes, and Quarantine, Practical Tips that Actually Work
- PODs: Use time-stamped, geo-tagged photo PODs where signatures aren’t feasible. Keep a standardized folder of PODs tied to the BL and invoice number for instant retrieval.
- HS Codes: Maintain a master HS for frequently imported SKUs, with product photography, and a recorded source for each classification (binding ruling, tariff lookup). Conduct quarterly audits for high-risk lines.
- Quarantine: For agricultural or animal products, verify accepted COE templates and pre-schedule an inspection timeframe at the port. Where allowed options, use a bonded movement to transport to an APHIS approved facility for treatment instead of risking on-dock destruction.
Read more: Automate Your Proof-of-Delivery Filing (POD)
Process & Tech: How Modern Ops Reduce Holds
The top secrets to success: Automation + human checkers. Getting pre-arrival filing ready whether it’s ACE / e-manifest, automating HS lookups, having document validation rules, and pre-alerting your customs broker decreases review. Don’t forget to share a single source of truth (central doc repository + e-POD collection) for customs, carriers and consignees to see the same record. For hold types and automated hold code (i.e .,statistical validation, 97H), work with a customs broker or your company to determine responses or required docs for each hold code.
If You Get Flagged: Triage Steps
- Pull the container file (invoice, BL, packing list, COOs, POD).
- Check the hold code (customs message) it tells you the missing piece.
- Supply missing document or request inspection release (bonded movement if available).
- Escalate to compliance or broker if duty/HS disputes risk a penalty.
Read more: 3PL vs. 4PL Providers: Which Is Right for Your Logistics Strategy?
Reduce Holds, Reduce Cost and Speed Time to Revenue
Improvements in data discipline can often prevent customs holds: complete invoices, accurate HS codes, unified Proof of Delivery, and established quarantine paperwork. Always view classification and pre-filing as part of your shipping SOP and more than just a final step. Centralize document storage, a simple digital capture of PODs and working with your broker can turn customs from a slow process to established outcome.
If you want help centralizing docs and automating pre-alerts for high-risk shipments, consider demoing a TMS that ties manifests, PODs, and classification records into a single shipment timeline. Tools that automate checks early are the fastest route to fewer customs flags.
