The Port of Mombasa is Kenya’s main seaport and handles containerized cargo, vehicles, bulk goods, etc. Clearing goods at Mombasa involves coordination with both KRA Customs and the Kenya Ports Authority (KPA), as well as sometimes the shipping line or consolidation agent.
Step-by-Step Port of Mombasa Clearance Process
- Appoint a Clearing Agent:
For sea freight, clearing and forwarding agent often helps coordinate clearance and payments on behave of the importer. The agent will usually need to present a release order from the shipping line – this comes after surrendering the original Bill of Lading and pay any outstanding freight or demurrage to the shipping agent to create a Customs entry in the iCMS/Single Window system. They will ensure the cargo is classified under the correct HS codes, and declare the value. If the shipment was insured and you have freight costs, those are added to the FOB value to get CIF (Cost, Insurance, Freight) which forms the customs value.
- Arrival of Cargo at the Port of Mombasa:
When your container or goods arrive by ship, they are listed on the ship’s manifest which is filed with KRA and KPA. You (the consignee) or your agent should have the Bill of Lading (B/L) from the shipper. Once the vessel arrives and is offloaded, KPA will stack the container in the port yard or transfer it to a Container Freight Station (CFS) if designated. You’ll typically be notified by your shipping line or freight forwarder of arrival and given a Bill of Lading exchange or delivery order.
At this stage, delays can begin if documents are missing or incorrect.
- Document Preparation and Verification:
Proper documentation is critical for smooth clearance. Required documents usually include:
Bill of Lading
Commercial Invoice
Packing List
Import Declaration Form (IDF)
Certificate of Conformity (CoC)
A professional clearing agent reviews all documents before submission to avoid errors.
At this stage, documents are verified early to prevent delays and penalties.
- Container Freight Station (CFS) allocation:
South Sudan cargos are moved from the port to a private off-port facilities (CFS) for clearance. Once the container is at the CFS, their facility fees apply.
- Customs Declaration with KRA:
After document verification, the clearing agent submits the customs declaration to the Kenya Revenue Authority (KRA) through the customs system. Mombasa’s system might assign the entry a channel (Green – no inspection, Yellow – document review, Red – detailed inspection). The agent prints a Customs Entry Form (also called Form C17 or Simplified Entry) which details the taxes. You then pay the import duties and levies as assessed. Payment is made to KRA’s designated bank or online payment, and the agent obtains the payment confirmation.
Any mistakes at this stage can result in fines or cargo being held.
- Cargo Inspection at Mombasa Port:
At Mombasa, customs will likely physically inspect the goods, especially if it’s a full container (FCL). They may open the container (or CFS) in the presence of the agent and/or importer if you wish and verify contents against the declaration. KEBS officers may verify that the contents with the conformity standards too.
This may include:
Physical inspection
Scanner inspection
Verification of declared goods
If you imported a vehicle, customs and KEBS will inspect the chassis/VIN, engine number, and general condition. KEBS will verify the Pre-shipment Inspection Certificate (e.g. by JEVIC or QIS for roadworthiness). If the car is too old (inspection, KEBS can reject it). For goods on pallets or cartons, they might do a partial/full check to verify sort of items.
KEBS might take samples (if needed; for example, food) & it is chemical items mandate. Other agencies on the port (similar to JKIA: Port Health, KEPHIS, etc.) will also have their turn if applicable. The container seal (placed on loading) will be checked for integrity. Always ensure the seal number matches what’s on the manifest/Bill of Lading.
- Port Charges and Release:
Before cargo release, port-related charges must be settled. These may include:
Port handling charges (varies by container or cargo type)
Storage charges (if clearance is delayed)
Port Charges and Shipping Line Charges:
Wharfage in container handling, usually charged on C&F/CIF of containerized cargo
If using a CFS, that station will charge handling and storage fees.
The shipping line may require payment of demurrage if the container is not collected within the free period (often 7-14 days after offloading) or your container could even be moved to a Customs Warehouse (ICB) as unclaimed cargo.
- Issue of Release Order:
If everything is in order, Customs will stamp Release on the entry documents or electronically release in the system.
KEBS and other agencies also issue a release if applicable. At this point, you’ll get a Release Order indicating the cargo is cleared.
- Gate Pass and Pickup:
The CFS or Port will issue a Gate Pass once they see that customs release and all port charges are paid. This gate pass is what allows the truck carrying your container or goods to exit the port/CFS gate.
You’ll need to arrange for a truck to pick up the container. If it’s a full container, it may be taken to your premises (you have limited time to unload and return the empty container to avoid extra charges). If it’s loose cargo (LCL – less than container load), the agent can pick from the goods warehouse.
Always ensure any permit (like an import license, CoC for standard, or other permits for import) is obtained in advance.
Clearance and Transport Cost
| CONT SIZE | CLEARANCE COST | ROARD TRANSPORT COST (MBS – ML – JUB) | MAX WEIGHT ALLOWED BOTH CONT. |
| 20TEU | $900 – $1,000 | $ 4,000 – $4,500 | 24 TONS |
| 40TEU | $ 1,100 – $1,200 | $ 4,000 – $4,500 |
NB: Charges for Shipping and CFSs vary depending on the shipping line and the CFS facility.
STORAGE CHARGES AS PER KPA TARRIF 2025
Free days allowed at port is 15 days thereafter below charges apply.
| TRANSIT | Remarshalling | 1-15 days | 16-21 days | Thereafter |
| 20TEU | $ 60 | Free | $ 30 | $ 50 |
| 40TEU | $ 90 | Free | $ 60 | $ 100 |