Customs Clearance Step-by-Step
Complete guide to clearing imported goods through Nigerian customs. From Form M to cargo delivery, understand the process, required documents, timelines, and port-specific considerations.
Last updated: 25 August 2026 | Reviewed by Calmwaters Shipping team
Overview
Nigerian customs clearance involves multiple steps, from opening Form M to cargo delivery. The process typically takes 5-15 days depending on port, documentation completeness, and cargo type. Using an experienced clearing agent can significantly reduce delays and ensure compliance.
Timeline
5-15 days
Duty Range
20-50% CIF
VAT
7.5%
Payment
Naira
Step-by-Step Process
Open Form M
Open Form M through a CBN-approved bank before vessel departs loading port.
Details:
- • Form M is mandatory for imports >$1,000 CIF
- • Open through CBN-approved bank
- • Submit before vessel departs loading port
- • Include: importer details, supplier details, goods description, value, payment terms
- • Valid for 12 months from date of issuance
Required Documents:
- • Company registration (CAC)
- • Tax Clearance Certificate
- • Bank details
- • Supplier details
- • Goods description
Timeline: 1-3 days
Port-Specific Notes:
Lagos Apapa
Process through any CBN-approved bank
Lagos Tin Can
Process through any CBN-approved bank
Onne
Process through any CBN-approved bank
Warri
Process through any CBN-approved bank
Calabar
Process through any CBN-approved bank
Tip: Ensure Form M is opened before vessel departs. Late submission can result in delays and penalties.
Ship Cargo and Obtain Bill of Lading
Ship the cargo and obtain the original Bill of Lading from the shipping line.
Details:
- • Ship cargo as per Form M specifications
- • Obtain original Bill of Lading (B/L) from shipping line
- • B/L serves as receipt, contract of carriage, and document of title
- • Verify B/L details match Form M specifications
- • Keep multiple certified copies
Required Documents:
- • Original Bill of Lading
- • Certified copies
- • Shipping instructions
Timeline: 1-7 days (transit time)
Port-Specific Notes:
Lagos Apapa
Major shipping lines available
Lagos Tin Can
Major shipping lines available
Onne
Limited direct services
Warri
Feeder services from Lagos
Calabar
Feeder services from Lagos
Tip: Verify B/L details immediately upon receipt. Errors on B/L can cause significant delays.
Submit Documents to NICIS II
Upload all required documents to the NICIS II platform for customs assessment.
Details:
- • Log into NICIS II platform
- • Upload Form M, B/L, invoice, packing list, certificate of origin
- • Upload product certification (SONCAP, NAFDAC) if applicable
- • Upload insurance certificate
- • Submit for customs assessment
Required Documents:
- • All required documents in digital format
- • NICIS II login credentials
Timeline: 1-2 days
Port-Specific Notes:
Lagos Apapa
NICIS II fully operational
Lagos Tin Can
NICIS II fully operational
Onne
NICIS II fully operational
Warri
NICIS II fully operational
Calabar
NICIS II fully operational
Tip: Ensure all documents are clear and legible. Blurred or incomplete uploads will cause delays.
Receive PAAR
Receive the Pre-Arrival Assessment Report from customs.
Details:
- • PAAR generated after NICIS II assessment
- • Contains assessed duty amount
- • Must be obtained before port entry
- • Processing takes 24-48 hours
- • Review PAAR for accuracy
Required Documents:
- • PAAR document
- • Assessment details
Timeline: 24-48 hours
Port-Specific Notes:
Lagos Apapa
PAAR processing at customs house
Lagos Tin Can
PAAR processing at customs house
Onne
PAAR processing at customs house
Warri
PAAR processing at customs house
Calabar
PAAR processing at customs house
Tip: Review PAAR carefully for any discrepancies in duty assessment. Challenge errors immediately.
Pay Import Duties and Levies
Pay the assessed import duties and levies through designated banks.
Details:
- • Pay duty in Nigerian naira
- • Payment through designated commercial banks
- • Keep all payment receipts
- • Duty calculated on CIF value
- • Total typically 20-50% of CIF value
Required Documents:
- • Payment receipts
- • Bank confirmation
- • Duty assessment
Timeline: 1-3 days
Port-Specific Notes:
Lagos Apapa
Multiple bank branches available
Lagos Tin Can
Multiple bank branches available
Onne
Bank branches available
Warri
Bank branches available
Calabar
Bank branches available
Tip: Ensure sufficient naira in account before attempting payment. Failed payments cause delays.
Physical Examination at Port
Present goods for physical examination at the port.
Details:
- • Three examination channels exist
- • Green channel: Documentary examination only
- • Yellow channel: Physical examination required
- • Red channel: Intensive examination required
- • Customs officials verify cargo against documentation
Required Documents:
- • Customs release note
- • Examination request form
- • All original documents
Timeline: 1-5 days
Port-Specific Notes:
Lagos Apapa
Congestion can cause delays
Lagos Tin Can
Moderate congestion
Onne
Generally faster processing
Warri
Generally faster processing
Calabar
Generally faster processing
Tip: Ensure cargo is accessible for examination. Hidden or blocked cargo causes delays.
Customs Release and Port Clearance
Obtain customs release after successful examination.
Details:
- • Obtain customs release note
- • Pay NPA dues and terminal handling charges
- • Obtain port clearance certificate
- • Complete all port documentation
- • Arrange cargo collection
Required Documents:
- • Customs release note
- • NPA payment receipt
- • Terminal handling receipt
- • Port clearance certificate
Timeline: 1-3 days
Port-Specific Notes:
Lagos Apapa
Higher port charges
Lagos Tin Can
Higher port charges
Onne
Moderate port charges
Warri
Lower port charges
Calabar
Lower port charges
Tip: Ensure all port charges are paid before attempting cargo collection.
Cargo Delivery
Arrange cargo delivery from the port.
Details:
- • Obtain gate pass from terminal
- • Arrange transportation (truck, container)
- • Verify cargo quantity and condition
- • Obtain delivery confirmation
- • Complete all documentation
Required Documents:
- • Gate pass
- • Delivery order
- • Transport documentation
- • Cargo receipt
Timeline: 1-2 days
Port-Specific Notes:
Lagos Apapa
Traffic congestion can cause delays
Lagos Tin Can
Traffic congestion can cause delays
Onne
Easier access
Warri
Easier access
Calabar
Easier access
Tip: Arrange transportation in advance. Last-minute arrangements can cause delays.
Duty Structure
| Component | Rate | Notes |
|---|---|---|
| Customs Duty | 5-35% | Based on product HS code |
| VAT | 7.5% | On CIF + duty |
| ETLS Levy | 0.5-5% | ECOWAS Trade Liberalisation Scheme |
| CISS | 1% | Combined Inspection Supervision Scheme |
| SONCAP | Variable | Standards certification |
Frequently Asked Questions
What is Form M and when is it required?
Form M is a mandatory customs document required for all imports into Nigeria valued above $1,000 CIF. It is opened through a CBN-approved bank and must be submitted before the vessel departs the loading port. Without a valid Form M, goods cannot be cleared through Nigerian customs.
How long does customs clearance take in Nigeria?
Customs clearance typically takes 5-15 days depending on the port, documentation completeness, and cargo type. Lagos Apapa: 5-15 days, Lagos Tin Can: 5-15 days, Onne: 7-20 days, Warri: 7-15 days, Calabar: 7-15 days. Clearance times improve significantly with proper documentation and experienced clearing agents.
What are the import duties in Nigeria?
Import duties in Nigeria are calculated on CIF value and vary by product type: Customs Duty (5-35%), VAT (7.5%), ETLS Levy (0.5-5%), CISS (1%), and other levies. Total duty rates typically range from 20-50% of CIF value depending on the product. Payments are made in Nigerian naira.
What documents are required for customs clearance?
Required documents include: Form M, Bill of Lading, Commercial Invoice, Packing List, Certificate of Origin, Product Certification (SONCAP for regulated goods), Insurance Certificate, and Import Declaration. Additional documents may be required for specific product categories.
What is PAAR and how do I get it?
PAAR (Pre-Arrival Assessment Report) is a document issued by Nigerian Customs after reviewing import documentation. It contains the assessed duty amount. PAAR is generated through the NICIS II platform after document submission and typically takes 24-48 hours to process.
What happens if goods are held at customs?
Goods may be held for several reasons: incomplete documentation, duty disputes, physical examination required, or regulatory compliance issues. Resolution depends on the specific issue, such as additional documentation, duty payment, or re-examination. Delays can be minimized by using experienced clearing agents and ensuring all documents are complete.
Need Help with Customs Clearance?
Our team at Calmwaters Shipping works with experienced clearing agents who can handle the entire customs clearance process. From Form M to cargo delivery, we ensure smooth, efficient clearance with minimal delays.
Contact us at info@westafricacharter.com or call +234 916 333 1144