When most people think of clearing goods in Nigeria, they only focus on the Customs Duty. However, the duty is often less than half of the total cash you need to exit the port. In 2026, the landscape has changed with the introduction of the 4% Import Levy (FCS) and updated terminal tariffs.
To avoid having your goods stuck at the port, you need a realistic budget. This guide breaks down every single fee you will encounter.
1. The Government Taxes (Customs Assessment)
This is the official bill from the Nigeria Customs Service. In 2026, this includes:
- Surface Duty: Based on your HS Code (usually 5%, 10%, or 20%).
- Surcharge: 7% of the surface duty.
- ETLS: 0.5% of the CIF value.
- Import Levy (FCS): 4% of the FOB value (this replaced the old 1% CISS).
- VAT: 7.5% of the total sum.
For a deep dive into these specific taxes, see our guide on Understanding Import Duties & Taxes.
2. Shipping Line Charges
Paid to the company that carried your goods (e.g., Maersk, MSC, Grimaldi).
- Shipping Agency Fee: Administrative cost for processing your Bill of Lading.
- Container Deposit: A refundable fee (approx. ₦200,000 to ₦450,000) to ensure you return the empty container.
- Terminal Delivery Order (TDO): The document that permits the terminal to release your cargo.
3. Terminal Handling Charges (THC)
Paid to the port operator (e.g., APMT in Apapa or Lekki Port). These cover the crane operations and moving the container within the yard. In 2026, these charges vary significantly between Apapa and the Lekki Deep Sea Port. Learn more about choosing the right port in our 2026 Practical Clearing Guide.
4. Professional Agency Fees
This is what you pay your clearing agent for their expertise. While negotiable, a professional agent in 2026 typically charges a flat service fee based on the container size or a percentage of the total value. Beware of “too-cheap” quotes that lead to hidden costs later.
2026 Estimated Budget for a 40ft Container
| Fee Category | Estimated Amount (₦) | Who Receives It |
|---|---|---|
| Shipping/Terminal Fees | ₦650,000 – ₦850,000 | Shipping Line/Operator |
| Customs Documentation | ₦120,000 | NCS Processing |
| Agency Service Fee | ₦150,000 – ₦250,000 | Clearing Agent |
| Container Deposit | ₦450,000 (Refundable) | Shipping Line |
*Note: These exclude the actual Customs Duty and VAT, which depend on the value of your goods. For help calculating those, use our 2026 Duty Formula Guide.*
Conclusion
Clearing a container in 2026 requires more than just a duty payment. By accounting for shipping, terminal, and agency fees upfront, you protect your business from the dread of underfunding. For the most current official rates, visit the Nigerian Ports Authority website.