South Sudan rejects Kenya’s new $5,000 container security fee

JUBA – South Sudan’s government has strongly protested a newly imposed USD 5,000 container security charge by the Kenyan authorities, saying the levy is crippling traders and worsening congestion at the Port of Mombasa, where hundreds of South Sudan-bound containers remain stranded.

The issue dominated a high-level meeting held in Juba between Trade and Industry Minister Atong Kuol Manyang, senior government officials and private sector leaders, amid growing fears that supply delays could trigger nationwide market disruptions.

Minister Atong said the government was taking the matter seriously and would not allow South Sudanese traders to be “unfairly burdened by foreign-imposed charges.”

“As the concerned ministry, we must call for urgent measures to ensure concrete solutions,” she stressed, adding that she had already briefed Vice President Dr James Wani Igga about the severity of the crisis.

Business representatives at the meeting urged stronger coordination among the Ministries of Trade, Finance and Transport, as well as the South Sudan Revenue Authority, to reduce overlapping taxes, changing shipping routes and unregulated clearing agents that have complicated the import process.

Long-criticised charges scrapped

In a key relief measure, Minister Atong announced the abolition of the USD 3,850 container tracking fee, popularly known as the OTP levy, which traders have long described as punitive and without a clear legal basis. She further promised a comprehensive review of all import-related fees and called for firm action against illegal charges imposed by unauthorised agents.

To streamline trade, the minister unveiled a national committee to review import taxes and pledged a nationwide tour of major trade hubs to consult traders directly.

Why South Sudan is outraged

In November, Transport Minister Rizik Zakaria Hassan revealed that Kenya had introduced a steep USD 5,000 security levy on every container destined for South Sudan—more than triple what importers to other regional markets are charged.

“For goods heading to Kenya, the fee is USD 1,000; to Uganda and the DRC, it is USD 1,500. But for South Sudan, the fee is USD 5,000, and that is within Kenya,” he said, describing the disparity as unjustifiable.

He warned that in many cases the combined cost of shipping, security and handling now exceeds the value of the goods themselves.

Chamber of Commerce chair Ladu Lukak also criticised Kenya’s decision to redirect South Sudan-bound cargo through Nairobi rather than shipping directly from Mombasa to Juba—a change that has pushed up handling fees by hundreds of dollars per container.

“As the chamber of commerce, we disagreed because it increases the cost,” he said, arguing the new routing and fees are driving many traders toward losses while destabilising the domestic market.