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What are the common problems with Transit customs?

The most frequent problems in transit customs are paperwork errors, misclassification/valuation disputes, border delays, and penalties for non-compliance. These issues affect shippers, freight forwarders and carriers who use transit regimes like TIR, NCTS, or ATA Carnets, and they can cause delays, added costs, and regulatory risk.


Documentation and Declarations


Proper documentation is the backbone of smooth transit. The following issues are among the most common hurdles that slow or derail shipments.



  • Incomplete manifests or packing lists that do not match the cargo.

  • Missing or inaccurate commercial invoices, including incorrect values or currency.

  • Wrong or missing importer/exporter identifiers (such as EORI numbers in the EU).

  • Incorrect or unapproved HS (Harmonized System) codes leading to misclassification.

  • Inaccurate valuation or failed disclosure of preferential origins and trade agreements.

  • Lack of required transit permits, licenses, or certificates for restricted goods.


Accurate, complete documentation reduces delays, minimizes hold times at borders, and lowers the risk of penalties.


Typical documents encountered in transit


Below are common documents used in transit regimes; errors here cascade into other steps of the process.



  • Commercial invoice and packing list

  • Transit declaration or TIR/NCTS documentation

  • Bill of lading or waybill

  • Licenses or certificates for controlled goods

  • Seals and related security documentation


Ensuring each document is accurate and properly aligned with the shipment helps maintain flow and compliance throughout the transit chain.


Border Delays and Inspections


Even well-prepared shipments can face delays once they reach border controls. Understanding the common causes helps stakeholders plan and communicate proactively.



  • Random or risk-based inspections that pause movement for verification.

  • Backlogs at border crossings or ports due to peak volume or staffing shortages.

  • Security checks, including seal verification and anomaly screening of cargo.

  • Discrepancies between declared goods and actual cargo triggering additional scrutiny.

  • IT system downtime or incompatibilities between customs portals and carrier/broker systems.

  • Delays caused by sanctions screening or additional compliance checks for high-risk destinations.


Prolonged border delays increase inventory carrying costs and can disrupt downstream distribution plans.


Inspections and risk management


Some inspections are routine; others are triggered by flags in the data matching process. Preparation and data hygiene help reduce the impact of inspections.



  • Pre-clearing data accuracy to minimize surprises at checks

  • Clear communication with border authorities about transit status

  • Contingency planning for potential delays and alternative routing

  • Maintaining traceable seals and tamper-evident security measures


Effective risk management and transparent data reduce the likelihood and impact of inspections.


Classification, Valuation, and Origin


Getting the tariff and origin right is crucial. Missteps here can trigger audits, higher duties, or retroactive charges.



  • Misclassified goods due to incorrect or outdated tariff codes

  • Under- or over-valuation of goods, intentionally or accidentally

  • Unclear or disputed country of origin, affecting preferential tariffs

  • Assumptions about transfer pricing or related-party valuation

  • Failure to apply duty reliefs, exemptions, or preferred trade agreements where eligible

  • Inaccurate measurement of quantity or weight, impacting duties and taxes


Misclassifications and valuation errors can lead to back duties, interest, penalties, and cargo holds during transit.


Systems, Data Integrity, and Interoperability


Transit relies on multiple actors and digital systems. When data doesn’t align across systems, shipments stall.



  • Inconsistent data between carriers, brokers, and customs authorities

  • Reliance on paper-based processes in environments pursuing digitalization

  • Data entry mistakes, duplications, or omissions in declarations

  • System outages or maintenance that disrupt electronic data exchange

  • Misalignment of commodity codes, document references, and transit identifiers

  • Insufficient integration with fiscal authorities for VAT/duty deferral schemes


Strong data governance, validated code lists, and reliable digital interfaces are essential to minimize friction in transit.


Technology and supplier readiness


Adopting reliable software, maintaining up-to-date tariff and regulatory databases, and testing data handoffs reduce delays and errors.



  • Regular updates of HS codes and origin rules in all systems

  • Automated checks for document completeness and consistency

  • End-to-end visibility across carriers, brokers, and customs

  • Training for staff on how to use electronic transit platforms


Technology readiness translates into smoother clearance and fewer holds during transit.


Compliance, Penalties, and Risk Management


Non-compliance can be costly and time-consuming. Understanding typical penalties helps organizations mitigate risk.



  • Fines for late or incorrect declarations and failure to present required documents

  • Seizure or detention of goods in cases of serious non-compliance or fraud

  • Interest and penalties on unpaid duties or taxes

  • Criminal charges in cases of intentional misrepresentation or evasion

  • Audits, post-clearance amendments, and potential reputational risk


Proactive compliance programs, routine internal audits, and timely updates to procedures help minimize penalties and disruptions.


Best Practices for Smoother Transit


To reduce the likelihood of problems in transit customs, organizations can adopt these practical approaches.



  • Pre-file data and obtain pre-clearance where available

  • Use accurate, standardized document formats and verifications

  • Maintain up-to-date tariff classifications and origin rules

  • Coordinate closely with carriers, brokers, and customs authorities

  • Invest in staff training on transit procedures and regulatory changes

  • Implement robust, end-to-end visibility and exception management


Adopting these practices improves predictability, reduces delays, and lowers compliance risk in transit operations.


Summary


Transit customs present a mix of paperwork, classification, valuation, and compliance challenges that can cause delays and extra costs. By ensuring complete and accurate documentation, maintaining data integrity across systems, understanding the triggers for inspections, and adopting best practices for compliance and data governance, shippers and forwarders can navigate transit regimes more effectively and minimize disruption to supply chains.

Kevin's Auto

Kevin Bennett

Company Owner

Kevin Bennet is the founder and owner of Kevin's Autos, a leading automotive service provider in Australia. With a deep commitment to customer satisfaction and years of industry expertise, Kevin uses his blog to answer the most common questions posed by his customers. From maintenance tips to troubleshooting advice, Kevin's articles are designed to empower drivers with the knowledge they need to keep their vehicles running smoothly and safely.