You have paid your customs duty. The money has left your account. Yet your cargo is still sitting at the terminal because the payment has not been confirmed on the system, and demurrage and storage charges keep adding up every day.

Here is what is being reported right now, and what you can do to protect your money.

What freight forwarders are saying

On 6 October 2026, the Africa Association of Professional Freight Forwarders and Logistics of Nigeria (APFFLON) raised the alarm over what it described as persistent delays in the processing and confirmation of customs duty payments made through GTBank. According to the association, these delays are leaving importers who have already paid exposed to demurrage, storage and terminal charges, and interest on borrowed funds.

APFFLON called on the Federal Ministry of Finance, the Nigeria Customs Service, the Nigerian Ports Economic Regulatory Agency, the Nigerian Ports Authority and the banks to act. Its requests include:

  • Real-time confirmation of customs duty payments
  • An emergency escalation channel for payments that do not reflect promptly
  • Protection from demurrage where there is verifiable evidence that duty has been paid
  • Consideration from terminal operators and shipping companies where delays are clearly caused by payment or system problems

These are the association’s concerns as reported on 6 October; watch for official responses from the bank and agencies involved.

Debit notes: another source of delay

Payment confirmation is not the only bottleneck. In a report published on 7 October 2026, the chairman of Blue Diamond Logistics China, which runs bonded terminal facilities in Lagos and Owerri, urged Customs to speed up the issuance and rectification of debit notes.

A debit note comes up when Customs directs you to pay an additional amount after your goods have been assessed. He said the process can sometimes take two to three days, and suggested it should be completed within one hour once an importer has been assessed. At the same time, he praised Customs’ B’Odogwu platform for speeding up clearance. In other words, the system is improving, but the remaining gaps are still expensive for importers.

Why a “small” delay costs so much

Once your free time ends, shipping line demurrage and terminal storage charges build up for every extra day your cargo stays at the port. If your payment takes three days to confirm and your free time is almost used up, those three days come straight out of your profit. If you need a refresher on how these charges work, read our guide to demurrage and storage charges in Nigeria.

What to do if your payment hasn’t reflected

  1. Keep every piece of evidence. Save your assessment notice, bank receipt or transfer confirmation, payment reference number, and the exact date and time you paid. Screenshots showing the payment status on the system also help.
  2. Escalate the same day. Ask your bank’s customs or collections desk to trace the payment, and have your clearing agent raise it with Customs at the command. Do not simply wait for it to “drop”.
  3. Write to the terminal and shipping line early. Inform them in writing, with your evidence attached, before the charges pile up. Ask for consideration on the days lost. There is no guarantee, but a timely, documented request is far stronger than a complaint made after you have paid.
  4. Know exactly when your free time ends. Confirm the free-time end date with both the terminal and the shipping line, so you know how much time you really have.
  5. Treat debit notes as urgent. If Customs issues a debit note, pay it as soon as it is generated and follow up until it is confirmed.

Evidence matters. In May 2026, the National Single Window management said terminal operators and shipping companies had agreed to review waiver requests case by case where importers could prove, with time, date and documents, that their consignment was directly affected by problems on the Single Window platform. That arrangement was specific to Single Window issues, but the lesson applies to any system delay: no proof, no case.

How to reduce the risk next time

  • Have funds ready before assessment. Moving money at the last minute adds delay on top of any confirmation problem.
  • Pay early in the day and early in the week. A payment made late on a Friday may not be resolved until the following week.
  • Ask your agent which payment channels are confirming quickly. Agents see payments go through every day.
  • Get your declaration right to avoid debit notes. An accurate HS code, value and description that match your commercial invoice reduce the chance of additional assessment. Our guides to HS codes and customs inspection explain why.
  • Don’t plan to clear on your last free day. Build a buffer of a few days into your timeline for problems like these.

Let us watch the clock for you

Delays outside your control are frustrating, but how quickly you respond still affects your final bill. At Septmax Logistics, we handle customs clearance every day and follow up on payments, debit notes and terminal charges so problems are raised before they become expensive. If your cargo is stuck or you want help planning your next clearance, contact our team.