Import Duties & Customs: Clearing Goods at Mombasa Port

Importing goods into Kenya through Mombasa Port is a critical process for businesses involved in international trade. Understanding the applicable taxes, levies, and compliance requirements ensures smooth clearance, avoids penalties, and supports operational efficiency. This guide breaks down the Import Declaration Fee (IDF), Railway Development Levy (RDL), customs clearing taxes, and how Adamjee Tax Experts helps businesses with audits and compliance in bonded warehousing.

What is Import Duty in Kenya?

Import duty is a government tax imposed on goods brought into Kenya from abroad. It is calculated based on the customs value of the goods. Ensure your invoices and shipping documents are eTIMS-compliant to avoid disallowed expenses under 2026 KRA rules.

Import duty is a tariff levied by the Kenya Revenue Authority (KRA) on imported goods. Its purpose is to generate revenue for the government and protect local industries from unfair competition. The duty rates depend on the type of goods, their value, and the applicable tariff schedule under the East African Community Customs Management Act.

From January 1, 2026, KRA requires that all imported goods have supporting eTIMS-compliant invoices; any import duty claimed on non-eTIMS invoices may be disallowed during audits. This emphasizes the need for meticulous documentation and proper customs classification.

For businesses clearing goods through Mombasa Port, understanding import duty calculation is essential. The KRA uses the CIF (Cost, Insurance, and Freight) value to determine the amount payable.

Learn more about our Tax Compliance Advisory services for guidance on import duty calculations.

Understanding the Import Declaration Fee (IDF)

The IDF is a mandatory 2% fee on the customs value of imported goods. Payment of the IDF is now strictly monitored via eTIMS, and non-compliance may trigger KRA penalties.

The Import Declaration Fee (IDF) funds the administrative costs of customs processing. It is charged on all imports except goods exempt under the Customs Act. The IDF must be paid before clearance, and the payment is linked to the release of the goods at the port.

In 2026, KRA has strengthened automated verification of IDF payments. Importers are advised to ensure their payment receipts are uploaded into the eTIMS system to avoid delays. Adamjee Auditors guides businesses in reconciling IDF payments with customs declarations, reducing the risk of penalties.

Explore our Audit & Assurance Services for audits related to import documentation and IDF verification.

Railway Development Levy (RDL): What You Need to Know

The RDL is 1.5% of the CIF value and funds railway infrastructure in Kenya. Businesses must include this in customs calculations and ensure proper documentation for eTIMS audits.

The Railway Development Levy (RDL) was introduced to finance the Standard Gauge Railway (SGR) and improve national logistics. It applies to all imports through Mombasa Port. Unlike IDF, RDL is strictly calculated as a percentage of the CIF value and is payable alongside other customs duties.

The 2025 Finance Act clarified that RDL payments are eligible for input verification in KRA audits, provided all receipts are captured in eTIMS. Adamjee Auditors assists clients in preparing documentation for both IDF and RDL compliance, ensuring smooth audits and clearance.

For businesses handling large volumes of imports, our CFO Advisory Services can integrate IDF and RDL into financial planning.

Customs Clearing Taxes: A Step-by-Step Guide

Customs clearing taxes include import duty, IDF, RDL, VAT, and excise duty (if applicable). Accurate classification and eTIMS-compliant invoices are critical to avoid disputes with KRA.

Clearing goods at Mombasa Port requires paying multiple taxes. Each tax has specific calculation methods and payment schedules:

1. Import Duty: Calculated on CIF value per tariff schedule.

2. Import Declaration Fee (IDF): 2% of CIF value.

3. Railway Development Levy (RDL): 1.5% of CIF value.

4. Value Added Tax (VAT): 16% of CIF + duties + IDF + RDL.

5. Excise Duty: Applicable on certain goods (e.g., alcohol, tobacco).

KRA now conducts real-time VAT and duty validation via eTIMS, reducing the tolerance for discrepancies. Adamjee Auditors ensures all customs invoices are validated, and our experts liaise with clearing agents for compliance.

Contact us for bespoke guidance on customs clearing taxes for your imports.

Role of Adamjee Auditors in Bonded Warehousing Audits

Adamjee Auditors provides specialized audits for customs bonded warehouses, ensuring regulatory compliance and accurate reporting under KRA 2026 eTIMS requirements.

Bonded warehouses store imported goods before duty and taxes are paid. Businesses must maintain meticulous records for goods in bonded warehouses, including:

• Receipts and invoices for all imported items.

• Proper segregation and storage according to customs classification.

• Timely reporting to KRA for audit purposes.

In 2026, KRA requires digital submission of warehouse records via eTIMS for audit verification. Adamjee Auditors conducts compliance audits, reconciles warehouse records, and advises on minimizing penalties and optimizing cash flow for duty payments. Our services ensure that imports in bonded warehouses are fully compliant, reducing the risk of fines.

Learn about our Bookkeeping Services to manage detailed warehouse records and financial reporting.

Common Challenges in Clearing Goods at Mombasa Port

Delays often arise from misclassified goods, incomplete eTIMS documentation, or unpaid duties. Adamjee Auditors helps identify and resolve these bottlenecks proactively.

Importers face several challenges:

1. Incomplete eTIMS invoices: Missing or inaccurate details can trigger penalties.

2. Incorrect tariff classification: Misclassification may result in overpayment or fines.

3. Delayed RDL or IDF payments: Can hold up the release of goods.

4. VAT disputes: Especially on mixed shipments with multiple tax categories.

Our experts perform pre-clearance audits and reconciliation of all import documentation. In 2026, KRA’s automated validation for VAT, IDF, and RDL means businesses must prepare accurate documentation in advance. This proactive approach minimizes delays and avoids penalties.

Explore our Payroll Services for related employee import benefits compliance.

eTIMS Integration and Compliance

eTIMS integration is mandatory for all import-related tax submissions in 2026. Ensure invoices, payments, and customs entries are fully synchronized to avoid disallowed expenses.

The Electronic Tax Invoice Management System (eTIMS) is KRA’s platform for automating invoice verification and customs compliance. From 2026, all expenses claimed must be traceable through eTIMS.

Adamjee Auditors assists businesses in integrating accounting systems with eTIMS, verifying all customs and duty-related transactions. We ensure that IDF, RDL, VAT, and other duties are captured accurately in financial statements. Non-compliance may result in disallowed expenses during audits.

Check our Offshore Accounting Services to manage multi-country import accounting with eTIMS compliance.

Optimizing Import Costs with Adamjee Advisory

Strategic planning of import duties, IDF, and RDL can reduce tax burdens legally. Adamjee Auditors provides advisory insights to optimize customs clearance costs.

Businesses can optimize import costs through:

• Proper HS code classification to ensure accurate duty rates.

• Timing imports to take advantage of KRA relief mechanisms, including the Automated Payment Plan (APP) for SMEs.

• Using bonded warehousing effectively to defer payments until goods are sold or consumed.

The KRA Automated Payment Plan (APP) in 2026 allows qualifying businesses to schedule tax payments, improving cash flow. Our experts advise on eligibility and compliance, helping companies navigate complex customs regulations.

Book a consultation with our CFO Advisory Services for financial strategies around import duty and customs taxes.

Best Practices for Smooth Customs Clearance

Maintain accurate eTIMS invoices, pre-validate payments for IDF and RDL, and schedule bonded warehouse audits to ensure smooth clearance at Mombasa Port.

To ensure efficient customs clearance:

1. Engage experienced clearing agents familiar with KRA regulations.

2. Prepare and reconcile all shipping and financial documents.

3. Validate IDF, RDL, and VAT calculations ahead of clearance.

4. Schedule regular audits of bonded warehouse stock.

5. Stay updated on KRA and 2025–2026 regulatory changes affecting import duties.

Our Training Webinars provide practical sessions on customs compliance, eTIMS integration, and bonded warehouse management, helping businesses build internal capacity and reduce reliance on external auditors.

Clearing goods at Mombasa Port requires a detailed understanding of import duty, IDF, RDL, and VAT, as well as adherence to eTIMS compliance rules. Businesses that plan ahead, maintain accurate records, and engage expert advisors like Adamjee Auditors can streamline import processes, reduce penalties, and optimize cash flow. From bonded warehouse audits to strategic tax planning, professional guidance ensures compliance with Kenya’s 2026 import regulations.

Navigate the complexities of compliance, tax, and financial management with a trusted partner. Adamjee Auditors, a member of Santa Fe Associates International (SFAI), provides world-class audit, tax, and advisory services to help your business achieve its goals.

Schedule a consultation with our expert team in Nairobi or Mombasa to discuss your business needs.

Nairobi Office  Park View Heights, Mombasa Road, OR Mbandu Complex, Langata Road
 +254 717 908 241
madamjee@adamjeeauditors.co.ke

Mombasa Office  Suite 401, Motorwalla Building, Jomo Kenyatta Road
 +254 750 053 053
info@adamjeeauditors.co.ke
https://adamjeeauditors.com/