Clearing Goods at Mombasa Port: A Step-by-Step Guide for Kenyan Importers

Mombasa port clearing is the process of getting your imported cargo declared to Kenya Revenue Authority (KRA), paying the duties and taxes due, passing any required standards checks, and collecting the goods from the Port of Mombasa. Most importers do it through a licensed clearing agent in Kenya, because KRA customs clearance goes through electronic systems that agents use daily. The process is manageable when your documents are accurate and your payments are ready, and it becomes expensive when paperwork is wrong and the container sits at the port.

This guide explains the general steps, the organisations involved and the practical habits that keep clearance smooth. It is general information. Procedures, systems and charges change, so confirm current requirements with KRA, the Kenya Ports Authority (KPA), the Kenya Bureau of Standards (KEBS) and your agent.

Who does what at the Port of Mombasa

It helps to know the main players before the ship arrives.

• Kenya Ports Authority (KPA) runs the port, including the terminals where containers are discharged and stored.
• Kenya Revenue Authority (KRA) runs customs. It assesses the declaration, collects duties and taxes, and decides whether cargo is released, checked or scanned.
• KEBS checks conformity to Kenyan standards for products that require it. Many goods from covered countries need a Certificate of Conformity from the exporting country, and goods without one can face inspection at the port.
• Shipping line issues the bill of lading and releases the container once its charges are settled.
• Clearing agent lodges the customs declaration, deals with the agencies and arranges collection on your behalf.
• Container freight stations (CFS) and inland container depots (ICD) are customs-licensed facilities where some cargo is moved for clearance or storage. Nairobi and Naivasha have inland depots, according to recent KPA and KRA announcements.

Step-by-step: how container clearing in Mombasa works

This is the usual path for container clearing Mombasa importers follow when cargo arrives by sea.

1. Get the documents early. Ask your supplier for the commercial invoice, packing list and bill of lading as soon as the goods ship. Add the KEBS Certificate of Conformity if your product needs one.
2. Appoint a licensed agent. Send the documents to your clearing agent, with your KRA PIN and importer details. Ask for a written list of charges.
3. The agent lodges the declaration. KRA has been moving cargo clearance onto its Integrated Customs Management System (iCMS), and your agent submits the entry electronically. Many import documents also pass through the national electronic single window run by KenTrade.
4. KRA assesses the entry. The tariff classification, declared value and origin are used to work out duty and taxes. KRA may release the goods, ask for more documents, or select the consignment for physical examination or scanning.
5. Pay duties, taxes and charges. Your agent will tell you the amount to pay and how. Keep every receipt.
6. Settle the shipping line and port charges. The shipping line releases the container, and the terminal charges for handling and storage must be cleared.
7. Collect and transport. When all approvals are in place, the container is gated out. You or your agent arrange a truck or rail transfer to your shop or warehouse.
8. Return the empty container on time. Shipping lines allow a set number of days for returning containers. Delays can lead to detention charges.

Treat this as a map, not a rulebook. The exact sequence and systems differ by cargo type, regime and the current instructions from KRA and KPA.

Import documents Kenya requires: what to prepare

Your agent will tell you what is needed for your specific goods, but the usual set of import documents Kenya customs expects includes:

• Commercial invoice showing the supplier, buyer, description, quantity, unit price and terms of sale.
• Packing list showing cartons, weights and contents.
• Bill of lading for sea freight, or air waybill for air freight.
• Certificate of Conformity, where KEBS requires it for your product, or an exemption certificate, waiver or Diamond Mark permit where one applies.
• Your KRA PIN and the agent's authority to act for you.
• Any special permits for regulated products. For example, certain food, chemical, electrical or telecom goods may need approval from the relevant regulator. Ask your agent which apply.

The key rule is consistency. The invoice, packing list and bill of lading must agree on quantities, descriptions and values. Our guide to the bill of lading, commercial invoice and packing list shows the usual errors to look for before the documents go to your agent.

Choosing a clearing and forwarding agent in Kenya

Clearing and forwarding Kenya is a competitive business, and agents vary in experience. KRA publishes lists of licensed customs agents and runs an annual licence renewal process, so start by checking that your agent appears on the current KRA list. Then ask practical questions:

• Before you hire any clearing agent Kenya importers recommend, ask: have you cleared this type of product before, and do you know its standards and permit needs?
• Can I have a written breakdown of your fees and of third-party charges such as port, shipping line and transport?
• Who will be my contact when there is a problem, and how quickly will you update me?
• Do you handle transport to my town, or only the customs step?

Be cautious with anyone who asks for cash payments with no receipt, will not give written quotes, or promises to make a problem disappear. Pay duties and taxes through official channels and keep proof. If you are unsure about a charge, ask the agent to show the KRA assessment.

Storage, demurrage and avoiding delays

The most common avoidable cost at Mombasa is time. Cargo that sits in the port beyond the free period attracts storage charges, and shipping lines charge demurrage and detention on containers kept too long. In November 2025, KRA and KPA announced measures to ease congestion, including moving long-stay cargo to customs-licensed facilities and referring to a five-day free storage period. Those arrangements may have changed, so ask your agent what free days and charges apply to your cargo now.

You can reduce delay by:

• Sending documents to your agent before the ship arrives, not after.
• Checking the documents for errors while the goods are still at sea.
• Having money ready for duties and taxes so payment does not hold the container.
• Confirming the KEBS requirement before you order, not when the cargo lands.
• Booking transport in advance for collection day.

Plan the cost of clearing, not just the freight

Clearance costs are part of your landed cost, along with freight, insurance, duties, taxes and transport. Our landed cost calculation guide shows how to add them up so you can price your goods realistically. Compare the shipping side with our freight to Africa guide, and if you are importing from China, read how to import from China to Kenya for the supplier and standards steps that come before the port.

Frequently asked questions

Do I have to use a clearing agent in Mombasa? Most importers do, because declarations go through KRA systems and require knowledge of classification and procedure. Ask KRA about the current rules for self-declaration.

How do I check that a clearing agent is licensed? KRA publishes lists of licensed customs agents on its website. Check the current list and ask the agent for their licence details.

What happens if my documents do not match? The declaration may be queried, delayed or corrected, and that can add storage and demurrage costs. Fix errors with the supplier early.

What is the difference between demurrage and storage? Storage is charged for cargo kept at the port or terminal. Demurrage and detention are charged by the shipping line for keeping the container beyond the free days. Ask your agent for the free periods that apply.

Do all goods need KEBS approval? Not all, but many imports do. Check with KEBS or your agent before ordering.

Can I clear goods in Nairobi instead of Mombasa? Some cargo is moved to inland depots under customs control. Ask your agent which route is available for your cargo.

Getting started

Before your next shipment, collect your documents early, check your agent against the KRA list, and agree charges in writing. If you want to compare offers from verified suppliers before you ship, post a sourcing request on Comilmart. Comilmart connects buyers with verified sellers across Africa, with no listing fees to get started. This is general information, so confirm requirements with the relevant authorities.