How Clearing Agents Charge at Mombasa Port

Updated 25 October 2026

Quick answer: there is no official price list for clearing agents at Mombasa. Each firm sets its own agency fee, so the only reliable figure is a written, itemised quote. What you can pin down is everything else on the bill: KRA’s taxes follow a fixed formula, and Kenya Ports Authority (KPA) charges come from its published tariff. Work out the taxes in our car import duty calculator, then use this guide to read an agent’s quote line by line.

What a Clearing Agent Actually Does

A clearing agent, formally a customs agent licensed by KRA, is the only party allowed to lodge your import entry on KRA’s customs system. For a car, the agent:

• Collects the bill of lading, invoice, export certificate and roadworthiness certificate from you.
• Lodges the entry, which triggers KRA’s tax assessment from the CRSP.
• Tells you how much to pay KRA, and confirms when it has been received.
• Pays or passes on port charges to KPA and the shipping line, and handles verification.
• Collects the car once the release order is issued and, if agreed, delivers it.
• Passes the vehicle’s details to NTSA so you can register it on eCitizen.

The Parts of a Clearing Bill

The KPA figures come from the KPA Tariff 2025, effective 15 September 2025. Storage days run consecutively from the day after the car is discharged, weekends and public holidays included.

Why Agency Fees Vary

An agency fee covers the agent’s time, staff at the port and their profit. Firms price it in different ways: a flat fee per car, a fee that rises with the car’s value, or a package that bundles port charges and transport. Because packages hide individual items, two quotes can look far apart while covering different things. Always ask each agent to separate:

1. Taxes payable to KRA (should match the calculator closely)
2. KPA and shipping line charges (should match published tariffs and the line’s invoice)
3. The agent’s own fee
4. Optional extras such as transport to Nairobi or number plate fitting

Only item 3 is truly negotiable. If an agent will not separate it, treat that as a warning sign.

How Long Clearing Takes

When documents are complete and taxes are paid promptly, clearing usually fits within the five free storage days. Delays come from missing documents, a CRSP query, or waiting for the buyer to raise the tax money. Every day beyond the free period adds storage, so have funds ready before the ship docks. Our guide to how long shipping a car from Japan takes covers the full timeline.

How to Check an Agent Before You Hire Them

• Licence: ask for the firm’s registered name and confirm it holds a current KRA customs agent licence. Our guide on clearing and forwarding licences explains how licensing works.
• Company registration: the name on the quote, the licence and the bank account should match.
• Physical office: a real firm has an office address in Mombasa or Nairobi you can visit.
• Payment: taxes are paid to KRA through official channels. Never send tax money to an agent’s personal account or M-Pesa number.
• References: ask for two recent customers who imported a similar car.

Red Flags

• A quote with one lump sum and no breakdown.
• A “duty” figure far below what the calculator shows. KRA’s assessment will be higher, and you will be asked for more later.
• Requests for “facilitation” money to speed up release.
• Pressure to pay everything up front before the ship has arrived.
• No licence number, or a name that differs from the bank account.

Can You Clear a Car Yourself?

Not on the customs system. Only licensed customs agents can lodge entries, so individuals need an agent even if they handle the rest of the paperwork. You can, however, pay KRA directly, check the KPA charges yourself and register the car on eCitizen once it is released.

Frequently Asked Questions

Is the agency fee included in KRA’s taxes?

No. KRA’s taxes go to KRA. The agent’s fee is a separate private charge.

Do I pay VAT on the agent’s fee?

A VAT-registered agent will add 16% VAT to its own fee. Ask whether the quote is inclusive or exclusive of VAT.

Want quotes? Use the form below. We keep your request and reply with options; we do not pass your details to any agent without asking you first.