Customs Clearing at Apapa & Tin-Can Island — What to Expect in 2026
Your container has arrived in Lagos. The clock is ticking. Every extra day at the port costs you money in demurrage — and some importers lose more to port delays than they do to duty. Here is exactly what happens, and how to get through it without the surprises.
The Lagos Port Complex: Apapa vs Tin-Can Island
The Port of Lagos is the largest and busiest port in West Africa. It comprises two main terminals relevant to most importers:
- Apapa Port: The original and largest Lagos port. Handles containers, bulk cargo, and liquid bulk. Notorious for access road congestion.
- Tin-Can Island Port: Located on the western end of Lagos Island. Generally considered slightly easier to access than Apapa. Also handles containers and RoRo (Roll-on, Roll-off) vessels for vehicles.
As of March 2026, both ports are pricing competitively, with similar terminal handling charges. Your freight forwarder will advise which terminal your vessel is calling based on the shipping line's schedule.
A third option gaining traction is the Lekki Deep Sea Port, built by Chinese investors, with an annual capacity of 1.2 million standard containers. Some importers are now routing through Lekki to avoid traditional port congestion.
The Clearance Process Step-by-Step
Here is what happens from vessel arrival to final delivery:
Your clearing agent should have your documents ready before the vessel arrives: Form M, Bill of Lading or Airway Bill, Commercial Invoice, Packing List, SONCAP Certificate (if applicable), and CCVO. Any document gap at this stage causes delays.
The shipping line files the cargo manifest with NCS. Your agent matches your goods against the manifest. Any discrepancy between the manifest and your Bill of Lading must be resolved — this alone can take 2–5 days.
Your licensed clearing agent files the SGD via the B'Odogwu system. This includes your HS code, declared CIF value, and calculated duties. B'Odogwu automatically applies the current CBN exchange rate.
NCS reviews your SGD. They may accept your declared value (best case) or query it and issue a higher assessment. If queried, your agent can provide additional documentation to support the declared value — or pay under protest and apply for a refund later.
Once the assessment is final, you pay duty at a designated bank. Payment is electronic. The bank transfers to NCS's CBN pool accounts. You receive a duty payment receipt (DPR).
NCS may select your container for physical examination — either a 100% strip examination or a document check. Examination typically takes 1–3 days. If your goods match your declaration, you proceed. If discrepancies are found, further assessments apply.
Once duty is paid and examination (if any) is complete, your container is released. You can then arrange final delivery by truck to your warehouse.
Typical Clearance Timeline
With clean documentation and no examination: 3–7 working days.
With valuation dispute or examination: 2–6 weeks — or longer if the matter escalates to the Customs Area Controller.
Demurrage: The Silent Killer
Demurrage is the charge levied by the shipping line when your container stays at the terminal beyond the free days. Free days are typically 7–14 days from vessel discharge, depending on your shipping line and terminal.
After free days, demurrage charges start — and they compound daily. A typical demurrage rate for a 20ft container is $50–$150 per day. For a 40ft container, $80–$200 per day. A 30-day delay on a 40ft container can cost $2,400–$6,000 in demurrage alone — often more than the import duty itself.
Choosing a Clearing Agent
In Nigeria, you legally cannot clear your own goods at the port — you must use a licensed customs clearing agent registered with the Nigeria Customs Service and the Council for the Regulation of Freight Forwarding in Nigeria (CRFFN). Red flags to avoid:
- Agents who claim to have "special connections" to reduce duty (this is bribery, and your goods can be seized)
- Agents who request cash payments without receipts
- Agents who are not registered with CRFFN
- Agents who quote unrealistically low clearing fees (they typically make up the difference in undisclosed charges)
The B'Odogwu System (2026)
NCS now operates the B'Odogwu unified customs management system, which replaced the older NICIS platform. Key things to know:
- All SGD filings, duty assessments, and CBN rate updates happen through B'Odogwu
- Exchange rates are automatically transmitted from CBN — your agent cannot manually input a rate
- The system is connected to FIRS (for VAT), the CBN, and designated banks for duty payment
- Digital pre-clearance is available — some agents submit SGDs before the vessel arrives, significantly cutting clearance time
Know Your Duty Bill Before Your Goods Arrive
Pre-calculate your full duty with 3 NCS valuation scenarios so you can have funds ready before demurrage starts.