How to clear goods at Mombasa Port: steps, fees and timelines

At a glance

Who handles it	A KRA-licensed customs (clearing and forwarding) agent. This is required for commercial imports.
Systems	KRA's iCMS for the customs entry; the KenTrade single window for permits
Main levies	Import Declaration Fee 2.5% and Railway Development Levy 2% of customs value, plus import duty (0–35%) and VAT
Standards check	KEBS certificate of conformity, or destination inspection at 0.6% of customs value ($300 minimum, $3,500 maximum)
Free port storage	First 5 days for domestic import containers, starting the day after discharge
Typical time	A few days if documents are ready and cargo goes on the green channel

Mombasa is East Africa's busiest port and the gateway for most of Kenya's imports, plus cargo heading on to Uganda, Rwanda, South Sudan and eastern Congo. Clearing goods there involves several bodies: the Kenya Revenue Authority (KRA) for customs and tax, the Kenya Ports Authority (KPA) for handling and storage, the Kenya Bureau of Standards (KEBS) for quality, and your shipping line. This guide explains who does what, what it costs and where delays usually happen.

Before you start: documents checklist

KRA lists these documents to support a customs declaration:

• Commercial invoice, showing the price you paid
• Packing list
• Bill of lading (sea freight) or airway bill (air freight)
• Import Declaration Form (IDF)
• Licences or permits, where your goods need them
• Exemption or remission authority, if you are claiming a tax exemption
• Any other document that supports the declaration, such as a KEBS certificate of conformity

You will also need a KRA PIN, either your own or your company's. If you do not have one yet, see our guide on how to get a KRA PIN.

Step by step

1. Appoint a KRA-licensed customs agent

   Choose a clearing and forwarding agent licensed by KRA before your goods ship. The agent has access to iCMS and takes legal responsibility for the accuracy of your declaration. Ask for a written quote that separates their agency fee from the government charges they pay on your behalf.

   Where: Before shipment · Cost: Agent's fee (negotiated) · Time: 1–2 days

2. Check whether your goods need a KEBS certificate or permits

   Many goods need a certificate of conformity from the Kenya Bureau of Standards (KEBS) programme before shipping. Some also need permits from other agencies, such as for food, medicines or chemicals. Your agent applies for permits through the KenTrade single window.

   Where: KEBS, KenTrade, the relevant agency · Cost: Varies by agency · Time: Days to weeks, so start early

3. Collect your shipping documents

   Get the commercial invoice, packing list and bill of lading (or airway bill) from your supplier and shipping line, plus any licences, permits or exemption letters. Send clear copies to your agent as soon as the goods ship.

   Where: Supplier and shipping line · Cost: Included in your purchase · Time: While goods are at sea

4. Let the agent lodge the entry on iCMS

   Your cargo must appear on the ship's manifest in iCMS. The agent then lodges your import declaration against that manifest, using your documents to set the customs value and tariff code.

   Where: KRA iCMS (online) · Cost: Agent's fee · Time: 1 day

5. Pay duties, taxes and levies

   iCMS calculates what you owe: import duty at the East African Community tariff rate for your goods, VAT, the Import Declaration Fee (2.5%) and the Railway Development Levy (2%) of the customs value, and excise duty where it applies. Under iCMS, the entry is passed automatically once you have paid.

   Where: Through iCMS-generated payment slip · Cost: Depends on value and tariff code · Time: Same day once paid

6. Go through verification

   KRA assigns each entry a risk channel. Green means direct release, with a possible audit later. Yellow means a cargo scan and a full document check. Red means a 100% physical inspection. KEBS may also inspect goods that arrive without a certificate of conformity.

   Where: Port, container freight station or ICD · Cost: KEBS destination inspection fee if it applies · Time: Hours (green) to several days (red)

7. Pay port charges and take delivery

   Settle Kenya Ports Authority charges and any shipping-line charges, get the release order and move your cargo out. Keep an eye on the free days: storage and demurrage start to add up fast after them.

   Where: KPA and your shipping line · Cost: Storage from $30/day (20ft) after free days · Time: 1 day

Costs and fees

There are three kinds of cost: government taxes, port and shipping charges, and your agent's fee. The government figures below are the published rates. Your actual bill depends on the customs value and tariff code of your goods.

Sources: PwC Kenya tax summary (reviewed July 2026), KPA Tariff clause 18, USDA FAS report on KEBS inspection. Checked 30 September 2026.

Charge	Rate	Paid to
Import duty	0% to 35% of customs value, depending on the goods (EAC Common External Tariff)	KRA
Import Declaration Fee	2.5% of customs value	KRA
Railway Development Levy	2% of customs value	KRA
VAT	Standard rate 16%, on the value including duty	KRA
Excise duty	Only on some goods, such as vehicles, alcohol and tobacco	KRA
KEBS destination inspection	0.6% of customs value, min $300, max $3,500 (if it applies)	KEBS
KPA storage, 20ft container	Free for 5 days, then $30/day to day 21, then $50/day	KPA
KPA storage, 40ft container	Free for 5 days, then $60/day to day 21, then $100/day	KPA
Shipping line demurrage	Set by each shipping line; check your bill of lading terms	Shipping line
Agent's fee	Negotiated with your agent	Customs agent

KPA's free days start the day after your container is discharged from the ship, and they run straight through weekends and public holidays. A container discharged on a Friday has used up most of its free time by the following Wednesday.

How long it takes

Situation	What to expect
Best case	Documents ready before arrival, duties paid promptly and a green channel release. The goods can leave within the five free days.
Typical	A yellow channel scan and document check adds time. Allow roughly a week and keep in touch with your agent daily.
Worst case	A red channel physical inspection, a missing permit or certificate of conformity, or a valuation dispute. This can take weeks, while storage and demurrage keep adding up.

For comparison, the government's Info Trade Kenya portal puts its step-by-step procedure for clearing a new commercial vehicle at between 2 hours 40 minutes and 6 days of processing, not counting time lost to missing documents.

Common mistakes and how to avoid them

• Waiting for the ship to arrive before starting. The five free days go quickly. Send your agent the documents as soon as the goods ship, so the entry is ready when the container lands.
• Under-declaring the value. KRA can reject the invoice value and assess its own. That leads to delays, extra tax and possible penalties. Declare the real price.
• Shipping regulated goods without a KEBS certificate. Check before shipping whether your goods need a certificate of conformity. Without one, you face destination inspection and possibly penalties.
• Mixing up KPA storage and shipping-line demurrage. They are separate charges with separate clocks. Clearing within one free period does not mean you are inside the other.
• An agent quote that bundles everything. Ask your agent to list the government charges separately from their own fee, and to share the iCMS assessment so you can see what KRA actually charged.

Alternatives and importing from abroad

• Clear inland instead. Containers can be moved to an inland container depot, such as the one in Nairobi, and cleared there. KPA gives domestic import containers five free days at ICDs as well.
• Transit cargo. Goods passing through Kenya to Uganda, Rwanda, South Sudan or the DRC follow transit procedures and get 15 free days of KPA storage.
• Small parcels. Low-value parcels sent by courier or post follow simpler procedures. Ask the courier how duty is charged.
• If you are overseas. You can appoint a licensed agent in Mombasa remotely and send documents electronically. Choose an agent you can check, and pay government charges against the official iCMS assessment.

Official links

• Kenya Revenue Authority: customs, iCMS and the list of licensed customs agents
• Kenya Ports Authority: tariffs, notices and cargo tracking
• Kenya Bureau of Standards: certificate of conformity and destination inspection
• KenTrade: Kenya's electronic single window for trade permits
• Info Trade Kenya: official step-by-step trade procedures

Frequently asked questions