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Quick Guide to Paying Mombasa Port Charges on eCitizen

Daisy MoraabyDaisy Moraa
September 24, 2025
Reading Time: 4 mins read
How To Apply For Temporary Storage At The Mombasa Icd

A collage image of a phone screen showing eCitizen portal and cargos at the Mombasa port. PHOTO/KPA

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Importers using the Port of Mombasa can now settle their port charges online through the government’s eCitizen platform.

Through e-Citizen, agents can access services that were previously offered across various independent systems from one single point.

The KPA e-citizen platform has offered flexibility to customers, who previously relied solely on banks for settling their bills, to choose to make payments through the M-Pesa platform, a mobile payment app integrated into their mobile phones, and the e-citizen platform.

Steps to Pay Mombasa Port Charges via eCitizen

1.Log in or register on eCitizen:
Go to the eCitizen portal (ag.ecitizen.go.ke) and sign in with your credentials. If you don’t have one, register with your Kenyan ID number.

2. Find the Relevant Service:
Use the ‘Search or Browse Services’ section to locate the Kenya Ports Authority (KPA) service.

3. Generate the Invoice / Reference:
Once you select the correct KPA service, the system should generate an invoice or payment reference. This reference is what you’ll use to make the actual payment. It includes details like your container number or manifest number.

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Also Read: How to Track Mombasa Port Cargo Online via eCitizen


4. Pay via eCitizen Payment Options:
eCitizen supports multiple payment channels. You can pay using:

    • Mobile money (M-Pesa or equivalent) using the eCitizen Paybill number (222222) and the reference/account number from your invoice.
    • Bank transfers or mobile banking if your bank supports eCitizen payments.
    • Other options, depending on the system (such as digital wallets or integrated banking apps), can be accessed via the eCitizen payment gateway.

5. Receive Confirmation / Receipt:
After payment is successful, a receipt or confirmation should be available on eCitizen. Download or print this. It will serve as proof of payment.

6. Submit Proof to Mombasa Port Authorities/ Clearing Agent and Proceed with Cargo Release:
With your proof of payment, either directly or via your clearing agent, present it to KPA and any other agencies (customs, etc.). Once all dues are cleared, the release order (Delivery Order) and gate pass can be issued.

Overview of Mombasa Port

The Port of Mombasa is Kenya’s largest seaport and the main gateway for international trade in East and Central Africa.

Situated on the Indian Ocean coastline, it serves not only Kenya but also its landlocked neighbors, such as Uganda, Rwanda, South Sudan, and parts of the Democratic Republic of the Congo.

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Also Read: Possible Delay at Mombasa Port as KPA Announces Changes in Shipping Schedules


Managed by the Kenya Ports Authority (KPA), the port operates as a hub for containerized cargo, bulk goods, petroleum products, and vehicles.

Its strategic location and deep natural harbor enable it to handle large vessels and increasing cargo volumes every year.

Linked to the Standard Gauge Railway and the national highway network, the port remains a critical driver of regional trade and Kenya’s economic growth.

Follow our WhatsApp Channel and X Account for real-time news updates.

How To Pay Port Charges At Mombasa Port
A photo of the Mombasa port. PHOTO/KPA

 

Tags: KPAMombasa port
Daisy Moraa

Daisy Moraa

Daisy Moraa is an all-round journalist at The Kenya Times, covering education, business, politics, and health. She specializes in storytelling, news reporting, and content creation, with experience across both mainstream and digital media platforms. She actively champions for the Sustainable Development Goals (SDGs), focusing on mental health awareness and sustainability. She holds a Bachelor of Science in Communication and Journalism from Rongo University. She can be reached at [email protected].

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