Export Clearance Process at Mombasa Port: A Step-by-Step Guide for Exporters and Terms You Must Understand
Kenya’s main gateway for international trade, the Mombasa Port, requires exporters to follow a clearly defined clearance procedure. This ensures that goods leaving the country meet customs, regulatory, and shipping requirements. Exporting without following the legal process carries serious risks, including fines of up to Sh5 million and imprisonment for up to five years.
This guide covers everything you need. You will learn the step-by-step clearance process at Mombasa Port, the essential documents you must prepare, and the key shipping terms you must understand.
Key Takeaways
The Kenya Revenue Authority (KRA) and Kenya Ports Authority (KPA) have implemented joint reforms to transform Mombasa Port into a globally competitive trade hub through enhanced collaboration, digital transformation, and coordinated reforms.
Effective August 3, 2026, all containerized cargo destined for Kenyan ports requires a valid Advance Cargo Declaration (ACD) Reference Number, which must be endorsed on the Bill of Lading.
The ACD system has received more than 1,000 applications since its rollout, demonstrating growing uptake by traders and shipping stakeholders ahead of full implementation.
The KenTrade Single Window System integrates more than 40 government agencies for permit and licence processing.
About 40 per cent of containers handled at Mombasa Port are empty, while KRA collects customs revenue from only about 25 per cent of total containers, underscoring the need to optimise cargo flow.
Business Registration and System Set-Up
Before you can begin the export clearance process, you must have a legally registered business and set up the necessary online accounts.
Business Registration
Your business must be registered with a valid Kenya Revenue Authority (KRA) PIN and a county business permit. Company and business registrations are handled through the eCitizen platform.
KenTrade Single Window System
You must create an account on the KenTrade Single Window System, which integrates more than 40 government agencies for permit and licence processing. The system serves as a single-entry point for parties involved in international trade to lodge documents electronically, for processing, approvals and to make payments electronically for fees and levies due to the Government.
InfoTrade Kenya Portal
All processes can be completed through the InfoTrade Kenya portal, which allows you to access import and export information in just five minutes. The portal is managed by KenTrade, a State Corporation under the National Treasury established under the National Electronic Single Window System Act No. 25 of 2022.
Obtain Product-Specific Licences and Certificates
Depending on the goods you intend to export, various regulatory approvals may be required.
Agricultural Products
Apply for a phytosanitary certificate from KEPHIS (Kenya Plant Health Inspectorate Service). A phytosanitary certificate is required for horticulture, tea, coffee and any plant-based products.
Industrial Goods
Seek export licences from the relevant regulatory authority.
Certificate of Origin
Obtainable through authorised chambers or trade bodies. The Certificate of Origin verifies the country where a product was wholly obtained, produced, or substantially transformed, and is necessary for tariff benefits under trade agreements. Preferential certificates of Origin are obtained from KRA, while the Ordinary Certificate of Origin is acquired from the Kenya National Chamber of Commerce & Industry.
Specific Certificates for Different Products
- Phytosanitary Certificate from KEPHIS for horticulture, tea, coffee and any plant-based products.
- Sanitary Certificate from Veterinary Services for fish, meat and any food item.
- Fumigation Certificate if required for wood articles, some gift items.
- Export Permit given by Mines and Geology Directorate for minerals including soapstone.
- Kenya Bureau of Standard Certifications.
Applications for these permits are submitted electronically through KenTrade at infotradekenya.go.ke.
Engage a Licensed Clearing Agent
Kenyan law requires exporters to work with a KRA-licensed clearing agent to handle customs documentation. A list of licensed agents is available on the KRA website.
Why You Need a Clearing Agent
The clearing agent handles the documentation and online declarations required by the Kenya Revenue Authority (KRA). The clearing agent gathers all mandatory documents: the commercial invoice, packing list, buyer’s contract, permits, and the exporter’s KRA PIN certificate. They are mandated to process the exportation documents in the customs system and assist in clearing goods on your behalf.
The appointed clearing and forwarding agent then books the vessel space and gets the shipping order as well as custom entry along with all the permits using the InfoTradeKenya Portal or KenTrade Single Window system.
Prepare and Submit Export Documentation
The clearing agent then lodges an export declaration through KRA’s Integrated Customs Management System (iCMS). Supporting paperwork is uploaded for review by Customs and partner government agencies.
Shipping Instruction Deadlines
The shipping line or freight forwarder must submit the Shipping Instructions (SI) for the export shipment. To prevent delays, exporters should provide all necessary documentation to their clearing agent well in advance. Export documentation for shipments to countries with advanced customs filing requirements must be submitted no later than 48 hours prior to the vessel’s Estimated Time of Berth at the Port of Loading . Missing this deadline can result in delays and additional costs.
The Essential Documents for Export
1. Commercial Invoice
The commercial invoice is the foundation of every export shipment. It is the primary document customs authorities use to assess duties, taxes, and admissibility. An international commercial invoice must contain seller and buyer names, addresses, and contact information, a detailed description of goods (product name, quantity, unit price, total value), Harmonized System (HS) codes for each product line, currency of the transaction and Incoterms, country of origin of the goods, and order or purchase order reference numbers.
Errors in this document cascade into every other step of the clearance process and can trigger audits.
2. Packing List
A packing list details the physical contents of each package in your shipment. It helps customs inspectors, warehouse staff, carriers, and your buyer verify that what was physically shipped matches what was commercially invoiced. It includes the number of packages, cartons, or pallets with identifying markings, net and gross weight per package and total shipment weight, dimensions and packaging type for each unit, and a description of contents per package, matched to invoice line items.
A well-prepared packing list speeds up customs inspection and reduces the likelihood that your shipment will be pulled for a detailed physical examination.
3. Certificate of Origin
A Certificate of Origin is one of the most heavily scrutinized trade documents in global commerce. It certifies the country where the goods were manufactured or substantially transformed. Customs authorities use it to determine tariff rates, eligibility under free trade agreements, and general import admissibility.
Types of Certificate of Origin include:
- COMESA Certificate of Origin for produce destined to COMESA countries.
- EUR – 1 Certificate of Origin for produce destined to European Union.
- GSP Certificate of Origin for produce destined to USA, Japan, Australia, Canada, etc.
- Ordinary Certificate of Origin for produce destined to Middle East, India, East Europe, etc.
- AGOA Certificate of Origin.
- EAC Certificate of Origin.
- AfCFTA Certificate of Origin for member states.
4. Bill of Lading or Airway Bill
This is the contract between you and the carrier. It serves as a receipt for shipped goods, a document of title, and evidence of the shipping contract.
- Ocean Bill of Lading: Used for ocean freight.
- Airway Bill: Used for air freight.
- Straight bill of lading: Used when the buyer has already paid for the shipment.
- Order bill of lading: Used when the shipment will be paid for at a later time. It is a transferable document of title.
Ensure that the details on your bill of lading exactly match those on your commercial invoice and packing list. Discrepancies are a primary trigger for customs holds.
5. Export License (If Required)
Certain goods, technologies, software, and destinations require an export license from the relevant regulatory authority. Although there is no overall export license, there are products which are highly regulated, and you must acquire the necessary export licenses or permits from the appropriate government agencies specific to your product.
6. Phytosanitary Certificate
A phytosanitary certificate from KEPHIS is required for horticulture, tea, coffee and any plant-based products. It confirms that the produce is pest- and disease-free.
7. Insurance Certificate
An insurance certificate provides proof that your shipment is covered against loss or damage during transit. Buyers, banks handling letters of credit, and some customs authorities may request this document before allowing clearance or releasing payment.
Mombasa Port Delivery, Stuffing, and Inspection
Once the export entry is approved, cargo is delivered to an approved Container Freight Station (CFS) or directly to the Mombasa port.
Stuffing and Inspection
Customs officials witness container stuffing, inspection, and sealing, recording seal numbers in the system. The process of stuffing, inspecting and sealing the cargo in the containers is done under the supervision of the customs officers either in an approved Container Freight Station or at the Port of Mombasa.
Pre-Advice of Port
Upon declaration to the customs, the clearing agent prepares a pre-arrival or receipt advice to the Kenya Ports Authority and pays all relevant charges, such as shore handling charges and wharfage charges.
Cargo Delivery
After clearance of the documents, the loaded truck delivers the cargo to the Port of Mombasa and receives a position slip before gaining entry to the port.
Customs Verification
Customs verification of the cargo is done through either physical inspection or scanning using X-rays, based on the risk assessment done by customs.
Advance Cargo Declaration (ACD): The New Requirement
The Kenya Revenue Authority (KRA) has introduced a new Advance Cargo Declaration (ACD) system for all containerized cargo destined for Kenyan ports .
Implementation Timeline
- Effective 03 August 2026: A valid ACD Reference Number must be obtained prior to cargo loading and endorsed on the Bill of Lading .
- Effective 01 September 2026: Vessel carriers will be required to validate the ACD Reference Number prior to loading and ensure containers are loaded at origin only when a valid ACD Reference Number has been obtained .
ACD Format
The ACD Number consists of a 15-digit alphanumeric format . For example: ACDKE2026004324
- ACDKE – 5-letter prefix reference name and country initials.
- 2026 – 4-digit year.
- 004324 – 6-digit sequential reference number received from KRA.
Processing Times
KRA’s review service-level agreement is 24 hours . However, the Authority says applications will normally be processed within two to three hours, while straightforward applications can take approximately 15 minutes . This means that in many cases, you can receive your ACD Reference Number very quickly, allowing you to finalize your shipping arrangements without delay.
Exemptions
Where the final destination shown on the Bill of Lading is outside Kenya and the consignee is also located outside Kenya, an ACD is not required, provided the Bill of Lading clearly identifies the movement as transit and shows the foreign final destination . This exemption is important for exporters shipping goods that are simply passing through Kenya to other markets.
How to Obtain the ACD Reference Number
- Register: Log into the official KRA ACD portal at https://acd.kra.go.ke.
- Submit Documents: Upload required documents to receive a draft ACD.
- Validate: Pay fees to receive the final validated certificate.
- Finalize BOL: Ensure the 15-digit ACD number is clearly printed on the final Bill of Lading.
Documents Required for ACD
- Draft Bill of Lading.
- Commercial Invoice.
- Freight Invoice.
- Export Declaration.
- Packing List (if necessary).
- Certificate of Origin (if necessary).
Non-Compliance
From 01 September 2026, only containers supported by a valid ACD Number will be eligible for loading. Shipments without a valid ACD Number may be rolled to a subsequent vessel and import customers may be subject to customs penalties and other regulatory actions for non-compliance.
Current Implementation Status
Since the ACD platform was rolled out on August 3, 2026, it has received more than 1,000 applications, demonstrating growing uptake by traders and shipping stakeholders ahead of full implementation.
Port Reforms and Operational Efficiency
The Kenya Revenue Authority (KRA) and Kenya Ports Authority (KPA) have reaffirmed their commitment to transforming the Port of Mombasa into a globally competitive trade hub through enhanced collaboration, digital transformation and coordinated reforms.
Empty Container Management
Empty containers will not be allowed into the port 24 hours before vessels berth for collection. Empty containers will be held in intermediate storage depots for a mandatory 72 hours before being allowed into the port for loading onto ships.
Long-Stay Cargo Evacuation
Long-stay consignments exceeding 21 days will be evacuated to Container Freight Stations for auction or destruction.
Container Freight Station Operations
CFS operators were urged to operate on a 24-hour, seven-day basis to support uninterrupted cargo evacuation, ease congestion and improve utilisation of available port space.
Smart Gate Initiative
KRA and KPA announced plans to commence the Smart Gate pilot at Gate 24, supported by enhanced integration between the Integrated Customs Management System (iCMS) and Partner Government Agencies. The Smart Gate initiative is expected to automate cargo movement, improve visibility across the supply chain, strengthen cargo security and reduce delays at port exit points.
24-Hour Operations
To enhance operational efficiency, KRA and KPA will harmonise staff shifts to guarantee continuous gate operations and facilitate cargo evacuation around the clock.
Key Port Statistics
The Port of Mombasa currently handles approximately 2.1 million Twenty-foot Equivalent Units (TEUs), making it a principal maritime gateway for the region. However, KRA noted that about 40 per cent of the containers handled at the port are empty, while the Authority collects customs revenue from only about 25 per cent of the total containers.
Export General Manifest and Final Clearance
Before the vessel departs, the shipping line files the Export General Manifest (EGM) with KRA, referencing the exporter’s entry number.
What is an Export Declaration?
An export declaration is a form detailing goods for customs clearance and trade stats. It notifies customs of goods leaving a country for trade statistics and controls. It is required for values over de minimis thresholds and includes HS codes, value, quantity, and origin. Electronic filing is mandatory in most nations.
Final Clearance
Once all checks are complete, KRA issues an Exit Clearance or Certificate of Export, authorising the goods to be loaded and shipped. The cargo is moved to the stacking yard for onward movement for loading into the ship.
Regional Electronic Cargo Tracking System (RECTS)
The Kenya Revenue Authority (KRA) has introduced a multi-vendor model for the Regional Electronic Cargo Tracking System (RECTS). Under this model, approved vendors will be responsible for the supply of electronic eSeals and Electronic Fuel Seals for cargo trucks and petroleum tankers under Customs control.
Eligibility Requirements for Vendors
- Valid certificate of incorporation and Communications Authority of Kenya (CAK) license for electronic tracking equipment.
- Valid tax compliance certificate and audited financial statements for the last three (3) years.
- Proven experience in vehicular/cargo tracking operations at a scale of not less than 1,000 units.
- Regional workshops and maintenance facilities within the EAC can service eSeals.
- Minimum stock of 1,000 operational eSeals available at all times.
How the Self-financing Model Works
The EAC RECTS self-owned model allows the service provider to have the uniquely identifiable e-fuel seals that shall be registered in the EAC RECTS platform. Approved Vendors own and maintain the seals and remain fully accountable to KRA for seal performance and integrity. The vendor will be jointly and severally liable for goods lost in transit if the seals do not report the non-compliant activity.
About the EAC RECTS
The Regional Electronic Cargo Tracking System (RECTS) was adopted by the East African Community (EAC) Secretariat as the EAC RECTS in 2022. KRA first established it in 2017 to enable real-time monitoring of cargo in transit and other Customs-controlled goods. EAC RECTS transmits critical alerts for any incident within 2 seconds of its occurrence. It also has uninterrupted reporting capability for at least 60 consecutive days on a single charge.
Export Terms You Must Understand
Understanding the language of international trade is essential for successful exporting.
Incoterms
Incoterms are internationally recognized rules that clarify the responsibilities of buyer and seller in a transaction, covering who arranges transport, who handles documentation, and where the risk transfers. They are regularly updated, so using the latest version (Incoterms 2020) is essential.
Key Incoterms to Know
EXW (Ex Works)
The only responsibility of the seller is to prepare the merchandise for the buyer, at his own premises, suitably packed for export shipping purposes. The buyer is responsible for all the charges and risks involved in the shipment of the merchandise from the moment it leaves the seller’s warehouse until it reaches its destination place. This term represents a minimum obligation for the seller.
FCA (Free Carrier)
The seller delivers goods to a carrier or location nominated by the buyer and is responsible for export clearance. This is suitable for multimodal transport. The seller is responsible for loading from warehouse, pre-carriage, and export customs clearance.
FOB (Free On Board)
The seller loads goods onto the buyer’s vessel at the port of origin. Risk transfers once goods are on board. This term is only for sea freight. The seller bears costs for packaging, loading from warehouse, pre-carriage, and export customs clearance. The buyer bears costs for handling at departure and main transport.
CFR (Cost and Freight)
The seller pays for transport to the destination port. Risk transfers once goods are loaded on the vessel. Exporters manage shipping costs but not insurance.
CIF (Cost, Insurance, and Freight)
The seller pays for transport and insurance to the destination port. The risk, however, transfers at the port of shipment. Incorporation of Institute Cargo Clause C, including “Minimum” insurance coverage. The seller bears costs for packaging, loading from warehouse, pre-carriage, export customs clearance, handling at departure, and main transport.
DAP (Delivered at Place)
The seller delivers the goods to a named place at the destination. The buyer handles unloading, import clearance, and pays duties and taxes. The seller bears costs for packaging, loading from warehouse, pre-carriage, export customs clearance, handling at departure, main transport, handling on arrival, and post-carriage.
DDP (Delivered Duty Paid)
The seller bears maximum responsibility, delivering the goods to the named destination, cleared for import, with all duties and taxes paid. The seller bears all costs including import customs clearance. This requires the seller to be registered for VAT or import duties in the buyer’s country, which can be complex for new exporters.
Best Practices for Using Incoterms
- Specify the Incoterm clearly in contracts (e.g., FOB Mombasa – Incoterms 2020).
- Always use the latest version; Incoterms 2020 is the current global standard.
- Coordinate with freight forwarders and customs agents to ensure compliance.
- Train export staff on the implications of each Incoterm.
- Align Incoterms with your export strategy—whether you seek full control or minimal involvement.
Working with Exporters
To successfully navigate the export process, it is helpful to connect with experienced players in the industry. For specific guidance on selling your produce, you can review a list of established avocado exporters who are actively buying from farmers and can provide market access. For more information, you can read our article on the list of top avocado exporters in Kenya.
Frequently Asked Questions
What is the export clearance process at Mombasa Port?
The export clearance process involves business registration, engaging a licensed clearing agent, preparing and submitting export documentation, cargo delivery and inspection, and final clearance through KRA’s iCMS system.
What is the Advance Cargo Declaration (ACD) system?
It is a new KRA requirement effective August 3, 2026, requiring a unique 15-digit ACD Reference Code for all containerized cargo destined for Kenyan ports. The code must be endorsed on the Bill of Lading before cargo is dispatched to Kenya.
What documents do I need to export through Mombasa Port?
You need a commercial invoice, packing list, certificate of origin, bill of lading/airway bill, export license (if required), and a phytosanitary certificate for plant-based products.
How do I register as an exporter in Kenya?
You must register your business through eCitizen, obtain a KRA PIN, create an account on the KenTrade Single Window System, and obtain product-specific licenses from relevant regulatory bodies.
What is the KenTrade Single Window System?
It is an online platform that integrates more than 40 government agencies for permit and licence processing. It serves as a single-entry point for parties involved in international trade to lodge documents electronically.
What is a phytosanitary certificate?
It is a certificate issued by KEPHIS confirming that the produce is pest- and disease-free. It is required for horticulture, tea, coffee and any plant-based products.
What are Incoterms?
Incoterms are internationally recognized rules that clarify the responsibilities of buyer and seller in a transaction, covering who arranges transport, who handles documentation, and where the risk transfers.
What are the current port reforms at Mombasa?
KRA and KPA have implemented reforms including the Smart Gate initiative, 24-hour operations, empty container management, and the evacuation of long-stay cargo exceeding 21 days.
How do I find a licensed clearing agent?
A list of licensed agents is available on the KRA website at https://www.kra.go.ke.
Where can I find a list of avocado exporters in Kenya?
For a list of top avocado exporters and to connect with potential buyers, you can read our article on the list of top avocado exporters in Kenya.
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Export clearance process at Mombasa Port guide 2026. Learn step-by-step procedures, required documents, and key export terms for Kenyan exporters.
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