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Kenya slashes cargo delays with COMESA e-certificate

By Phathisani Moyo, Senior contributor
Johannesburg, 09 Oct 2025
Kenya’s new electronic cargo clearance system is set to cut weeks-long border delays, making cross-border trade faster, cheaper, and more transparent across Eastern and Southern Africa.
Kenya’s new electronic cargo clearance system is set to cut weeks-long border delays, making cross-border trade faster, cheaper, and more transparent across Eastern and Southern Africa.

Kenya has taken a giant step toward faster and more efficient cargo clearance with the rollout of the COMESA Electronic Certificate of Origin (e-CO) .

The revolutionary digital platform replaces the slow and corruption-prone paper-based system that often kept goods stuck at border posts for up to two weeks awaiting clearance.

The new e-CO system enables exporters to apply for, issue, and verify certificates online, eliminating lengthy manual procedures that previously required physical paperwork, in-person verification, and courier delays. 

These certificates verify the origin of goods and determine whether they qualify for preferential trade within the COMESA Free Trade Area, which represents 21 African countries.

The e-CO was unveiled a day ahead of the ongoing 24th COMESA Summit of Heads of State and Government in Nairobi, running under the theme: “Leveraging digitalisation to deepen Regional Value Chains for Sustainable and Inclusive Growth.”

Regina Akoth Ombam, principal secretary in the Ministry of Industry, Trade and Investment, said the innovative platform demonstrates that Kenya is ready to drive forward digital transformation and regional integration. 

“The e-CO will eliminate inefficiencies, reduce paperwork, and foster transparency at every stage of the export process,” she said

Under the new system, the Kenya Revenue Authority will handle registration, issuance, and verification of certificates, while the COMESA Secretariat will provide technical support. 

The platform also removes the $3 manual certification fee, offering a cost-saving benefit to traders and small exporters.

Dr. Christopher Onyango, COMESA’s director of trade and customs, expressed his confidence that the new system will improve efficiency.

“The manual system led to long delays, inefficiencies, and even abuse. The e-CO is a game-changer that will ensure real-time verification, faster clearance, and fraud-resistant trade documentation,” he stated.

Kenya joins Eswatini, Malawi, Zambia, and Zimbabwe, which were among the first to digitise their cargo clearance systems under the COMESA Trade Facilitation Programme, funded by the 11th European Development Fund.

Cargo handling plays a crucial role in Kenya’s economy, with the logistics and freight sector contributing nearly 8% to the country’s GDP, according to the Kenya National Bureau of Statistics. 

Onyango emphasized that by digitising clearance, Kenya not only reduces border congestion and operational costs but also positions itself as a leader in regional digital trade under both COMESA and the African Continental Free Trade Area frameworks.

“Faster, safer, and smarter trade is no longer a dream but Kenya’s new reality,” he said.

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