All you Need to Know about the E-manifest Procedure by the Nigeria Custom Service

All you Need to Know about the E-manifest Procedure by the Nigeria Custom Service

Introduction

In an era where global trade is increasingly becoming digitized, Nigeria has continued to evolve its customs processes to align with international standards. One such development is the introduction of the Electronic Manifest (E-Manifest) by the Nigeria Customs Service (NCS)—a strategic initiative that promotes transparency, efficiency, and improved cargo clearance.

The E-Manifest is an integral part of the Nigeria Integrated Customs Information System (NICIS), designed to facilitate seamless reporting and clearance of cargoes entering and leaving the country through air, land, and sea ports.

This article explores the purpose, process, regulatory framework, challenges, benefits, and practical case study of the E-Manifest procedure in Nigeria. If you are a freight forwarder, shipping agent, customs broker, importer, or exporter, this guide is your go-to resource for understanding everything about the E-Manifest system.

What is an E-Manifest?

An E-Manifest is an electronic version of the cargo manifest that is submitted to customs authorities prior to the arrival or departure of a vessel, aircraft, or vehicle. It details the list of goods, consignments, container numbers, consignors, and consignees.

Unlike the traditional paper-based manifest, the E-Manifest is submitted through digital platforms, allowing for:

• Faster clearance

• Better data accuracy

• Enhanced customs risk management

In Nigeria, the E-Manifest is submitted via the Nigeria Integrated Customs Information System (NICIS) portal or Direct Trader Input (DTI) terminals.

Legal and Regulatory Framework

The E-Manifest procedure is governed by various laws and policy instruments, including:

1. Customs and Excise Management Act (CEMA) Cap C45 LFN 2004

2. WCO Revised Kyoto Convention

3. Nigeria Single Window Project

4. NCS Standard Operating Procedures on Cargo Manifest

5. Federal Government Executive Orders on Ease of Doing Business

These frameworks empower the Nigeria Customs Service to demand cargo manifest information before arrival for customs processing and risk profiling.

Objectives of the E-Manifest System

1. Promote Transparency: Eliminates falsified or altered paper documents.

2. Speed up Clearance: Reduces bottlenecks at ports by initiating early processing.

3. Improve Revenue Collection: Minimizes under-declaration and fraud.

4. Facilitate Trade: Supports Nigeria’s trade facilitation goals.

5. Enable Risk Profiling: Allows customs to profile cargoes for inspection before arrival.

6. Reduce Physical Contact: Encourages automation in line with global practices.

Who Should Submit the E-Manifest?

The following entities are required to submit E-Manifests:

• Shipping Lines and Agents

• Airlines and Air Cargo Agents

• Road Transport Operators (for cross-border trade)

• Freight Forwarders

• Terminal Operators

• Bonded Warehouse Operators

Mandatory Information Required in E-Manifest

An E-Manifest must contain accurate and complete details such as:

1. Carrier Information: Name of shipping line or airline

2. Vessel/Aircraft Number: Identification of transport vehicle

3. Port of Origin and Destination

4. Bill of Lading Number

5. Container Number (for sea cargo)

6. Description of Goods

7. Consignor and Consignee Information

8. Weight and Quantity

9. HS Code and Tariff Classification

10. Date and Time of Arrival

Step-by-Step Process for Submitting E-Manifest in Nigeria

Step 1: Registration

Before you can submit E-Manifests, you must register with the Nigeria Customs Service through:

• Customs Zonal Office

• Online DTI registration portal

• Authorized Service Providers (if using 3rd-party platforms)

Step 2: Manifest Preparation

Use a manifest preparation tool compatible with NCS NICIS portal. You can use:

• Nigeria Customs XML Schema

• Manifest Software (e.g., Cargowise, Asycuda)

Step 3: Upload via NICIS Portal

Login to the NICIS portal or use your DTI code to upload:

• Import Manifest (for arriving goods)

• Export Manifest (for outgoing goods)

The system auto-validates the content based on HS codes, ship schedule, and bill of lading.

Step 4: Acknowledgment and Validation

Once submitted:

• Customs will acknowledge receipt

• Manifest is validated electronically

• If there are errors, the system flags it for correction

Step 5: Manifest Matching

• Shipping documents are matched with declaration documents

• If there’s inconsistency, the system will delay the clearance

Step 6: Risk Assessment

The system assesses:

• Origin

• Type of cargo

• Importer/exporter’s risk profile

Cargoes that pass the risk threshold are given green light for fast-track.

Consequences of Non-Compliance

Failure to submit an E-Manifest or incorrect submission may result in:

1. Delayed Clearance

2. Sanctions and Fines

3. Cargo Demurrage Charges

4. Blacklist from Customs Portal

5. Customs Investigation or Seizure

Challenges in the E-Manifest System

Despite its benefits, challenges remain:

• Network Instability: Delays due to poor internet access

• Limited Technical Know-How: Many agents still lack digital skills

• System Downtime: Frequent portal errors or maintenance issues

• Incorrect Data Entry: Leads to validation failure

• Resistance to Change: Stakeholders still rely on manual submissions

Benefits of E-Manifest System

Case Study: How E-Manifest Helped Streamline Cargo Clearance at Apapa Port

Background:

ABC Shipping Limited, a logistics company based in Lagos, traditionally faced delays in clearing cargoes at Apapa Port due to paper-based manifest errors and duplication.

Challenge:

In Q1 2023, one of their major import consignments faced a 12-day delay due to inconsistent manifest records. They incurred ₦1.5 million in demurrage and warehousing fees.

Solution:

They adopted the E-Manifest system through the NCS portal, trained staff on NICIS usage, and partnered with a certified DTI agent.

Results:

• Clearance Time Reduced: From 14 days to 5 days

• Demurrage Cut by 80%

• Improved Relationship with Customs

• Zero Rejection of Manifests

ABC Shipping now submits all manifests electronically and encourages clients to comply with digital documentation.

How to Avoid Errors in Your E-Manifest Submissions

To minimize delays, follow these best practices:

1. Double-Check HS Codes

2. Ensure Consignee Name Matches Import Document

3. Avoid Abbreviations

4. Check for Accurate Container Numbers

5. Validate Cargo Descriptions

6. Use the Latest Software or Manifest Templates

7. Get Trained on NICIS and DTI Procedures

Recent Innovations in E-Manifest Management

Nigeria Customs has rolled out innovations like:

• Real-Time Manifest Synchronization

• Manifest Sharing Among Border Posts

• API Integration with Terminal Operators

• Artificial Intelligence for Risk Profiling

• E-Tracking of Manifest Submissions

These advancements have made the E-Manifest process more dynamic and responsive.

Role of Other Agencies in E-Manifest Clearance

Several government and port stakeholders rely on the E-Manifest system:

• Nigeria Ports Authority (NPA) – Uses E-Manifest to track vessel arrivals

• Nigerian Shippers’ Council (NSC) – Monitors freight efficiency

• Nigerian Immigration – For crew clearance

• NAFDAC / SON / NESREA – Cross-checks consignments with permits

• Terminal Operators – Plan unloading schedules based on manifests

Tips for Importers and Exporters

1. Work with Licensed Agents

2. Submit Documents Early

3. Follow Up with Customs and Terminal

4. Attend Customs Stakeholder Meetings

5. Adopt a Digital Compliance Culture

Future of E-Manifest in Nigeria

With the advent of the African Continental Free Trade Agreement (AfCFTA) and Nigeria’s digital customs roadmap, the E-Manifest system will likely evolve into:

• Blockchain-Integrated Manifests

• End-to-End Paperless Clearance

• Predictive Clearance Models

• Integration with e-Tax and e-Payment platforms

Conclusion

The Nigeria Customs Service E-Manifest procedure is a vital transformation tool for trade facilitation in Nigeria. By embracing the system, stakeholders reduce cargo dwell time, minimize fraud, and enhance transparency. With continued improvement and stakeholder cooperation, Nigeria’s ports and borders will become more competitive and efficient in global trade.

Call to Action

Are you an importer, exporter, or logistics operator looking to streamline your clearance and trade operations? At Chaman Law Firm, we offer customs compliance services, legal advisory on cargo documentation, and full representation before regulatory agencies.

Take Action Now – Stay Compliant, Stay Ahead!

Navigating Nigeria’s port systems doesn’t have to be complicated. With the E-Manifest system now mandatory for all cargo declarations, compliance is no longer optional—it’s essential.

At Chaman Law Firm, we offer professional legal and customs compliance services for importers, exporters, shipping companies, and freight forwarders. Whether you’re dealing with cargo clearance, documentation challenges, customs detentions, or system errors, we’ve got your back.

📌 Need help filing your E-Manifest correctly?
📌 Facing delays, penalties, or cargo seizures?
📌 Unsure how to comply with Customs NICIS or DTI procedures?

Let us handle the process for you—efficiently, legally, and professionally.

📞Phone:  08065553671, 08096888818

✉ Email: chamanlawfirm@gmail.com

📍 Address: 115, Obafemi Awolowo Way, Allen Junction, Ikeja, Lagos, Nigeria

🌍Click here to learn more about Chaman Law Firm

Let’s help you navigate the complexities of Nigeria’s E-Manifest system with ease.