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Customs & compliance

The nine most common customs clearance delays, and how to avoid each

Almost every delay we see traces to one of nine causes. All nine are preventable, and eight of them are preventable before the goods ship.

JubaLink Cargo · · · 3 min read

1. The importer is not properly registered

Why it happens: the buyer assumes registration can be handled while the goods are in transit, or that the clearing agent can clear in their own name.

What it costs: everything stops. Storage and detention run while registration is completed. (Kenya Ports Authority, verified 19 Oct 2026)

Prevention: register with the National Revenue Authority and obtain a TIN before placing the order. (South Sudan National Revenue Authority, verified 19 Oct 2026)

2. No Certificate of Conformity, and the goods need one

Why it happens: the buyer didn't check scope, or relied on a supplier unfamiliar with the programme.

What it costs: this is the worst one on the list, because the certificate is a pre-export document and cannot be obtained retrospectively.

Prevention: check scope at quotation stage; write the obligation into the purchase order. Read more

3. Documents that contradict each other

Why it happens: documents produced at different times by different people, never checked against each other.

What it costs: a verification query, typically days.

Prevention: the ten minute side by side check before shipping. Same consignee, same description, same quantities, same values. Document by document guide

4. A valuation query

Why it happens: a declared value that doesn't look like a real transaction, or one that cannot be supported with payment evidence. Customs determines value under the Customs Service Act. (South Sudan National Revenue Authority, verified 19 Oct 2026)

What it costs: often more in storage and detention than the duty ever at stake.

Prevention: declare the real price and keep the payment evidence with the file.

5. Classification disagreement

Why it happens: a vague description, or a code chosen for its rate rather than its accuracy.

What it costs: reassessment, and sometimes a penalty.

Prevention: classify before shipping, describe the goods properly, and use the same code on the export and import declarations. See classification

6. A sector permit left until arrival

Why it happens: the buyer didn't know the category was regulated. Pharmaceuticals, medical devices and food are the usual ones. (Republic of South Sudan, verified 19 Oct 2026)

What it costs: weeks, in some cases.

Prevention: identify regulated categories at the ordering stage. The Trade Information Hub lists procedures for many specific products. (Ministry of Trade and Industry, South Sudan, verified 19 Oct 2026)

7. A packing list that doesn't match the cargo

Why it happens: the list was generated from the purchase order rather than from what was actually packed.

What it costs: an examination that would have taken an hour takes a day, and a discrepancy may trigger a wider inspection.

Prevention: pack first, then produce the list from the packing. Number the pieces.

8. The consignee is unreachable

Why it happens: nobody nominated a contact with authority to answer queries or release funds.

What it costs: idle days, for no reason at all.

Prevention: nominate a reachable contact and tell your agent who they are.

9. Transit bond and seal issues

Why it happens: on transit cargo, a seal discrepancy, a route deviation, or documentation that doesn't reconcile at the exit point. (Kenya Revenue Authority, verified 19 Oct 2026)

What it costs: the movement is held and the bond is not discharged, which can become a liability long after delivery.

Prevention: record and photograph seals at every handover; never agree to an unapproved change of route or destination. See transit bonds

The pattern

Eight of these nine are settled before the goods ship. The ninth, an unreachable consignee, is settled with a phone call. None of them is really a border problem, even though all of them show up at the border.

If a consignment of yours is held up now, send us the entry reference and the documents and we will tell you which of the nine it is.

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Send us the cargo description, weight or volume, and the pickup and delivery addresses. We reply with a written rate, the transit time and the documents you will need.

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