Step-by-Step Process of Export Clearance at Mombasa Port

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.

To export goods through the Mombasa port, one has to engage a licensed clearing and forwarding agent to handle the documentation and online declarations required by the Kenya Revenue Authority (KRA).

Business Registration and System Set-Up at Mombasa Port

Before export clearance can begin, an exporter must have a legally registered business with a valid Kenya Revenue Authority (KRA) PIN and a county business permit.

Company and business registrations are handled through the eCitizen platform: https://www.ecitizen.go.ke.

The exporter must also create an account on the KenTrade Single Window System, which integrates more than 40 government agencies for permit and licence processing at https://www.kentrade.go.ke/single-window-system.

Obtain Product-Specific Licences and Certificates

Depending on the goods, various regulatory approvals may be required.

• Agricultural products: Apply for a phytosanitary certificate from KEPHIS.
• Industrial goods: Seek export licences from the relevant regulatory authority.
• Certificate of Origin: Obtainable through authorised chambers or trade bodies.

Applications for these permits are submitted electronically through KenTrade at https://infotradekenya.go.ke.

Engage a Licensed Clearing Agent

Kenyan law requires exporters to work with a KRA-licensed clearing agent to handle customs documentation.

Also Read: Quick Guide to Paying Mombasa Port Charges on eCitizen

A list of licensed agents is available on the KRA site at https://www.kra.go.ke.

Prepare and Submit Export Documentation

The clearing agent gathers all mandatory documents: the commercial invoice, packing list, buyer’s contract, permits, and the exporter’s KRA PIN certificate.

• The 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.
  More on iCMS can be found at: https://www.kra.go.ke/customs

Mombasa Port Delivery, Stuffing, and Inspection

Once the export entry is approved, cargo is delivered to an approved Container Freight Station or directly to the Mombasa port.

Also Read: Guide to Clearing Your Car at Mombasa Port

Customs officials witness container stuffing, inspection, and sealing, recording seal numbers in the system.

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.

Once all checks are complete, KRA issues an Exit Clearance or Certificate of Export, authorising the goods to be loaded and shipped.

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