Mombasa- Juba corridor grapples with rising costs and security fears

The Mombasa–Juba trade corridor, a vital artery for South Sudan’s cargo, is facing logistical challenges despite recent diplomatic approaches to solve the issues.

Shippers say the challenges have led to escalating costs and systemic inefficiencies that threaten to choke the movement of cargo to Mombasa's second-biggest transit market.

At the heart of the current crisis is a widespread failure to return empty shipping containers to Mombasa. At the Port of Mombasa, South Sudanese and Kenyan authorities have intensified collaboration to unlock the non-tariff barriers inhibiting the movement of cargo.

During a recent stakeholders’ forum hosted by the Kenya Ports Authority (KPA), South Sudan’s Ambassador to Kenya, Anthony Kon, said South Sudan will establish a consulate in Mombasa, a move aimed at promoting trade and streamlining business operations between the two nations.

The ambassador also appealed to the Kenyan government to extend visa deadlines for South Sudanese traders, allowing them more time to clear goods.

“Such a gesture would not only ease the burden on South Sudanese traders but also strengthen bilateral trade relations and enhance confidence in the Port of Mombasa as a preferred gateway for South Sudan’s imports and exports,” said Kon.

The South Sudanese Embassy in Nairobi had earlier issued an urgent appeal to importers to return containers that remain the property of shipping lines.

Many traders mistakenly assume these containers are part of their purchased goods, thereby withholding them in Juba and triggering serious consequences. This is as a result of the high container deposit asked by shipping lines, based on the risk associated with the delivery of the goods.

According to the Kenya Ports Authority KPA officials, the container deposits can go as high as US $5,000 (Sh645,700) compared to the $1,000 (Sh129,140) charged to Ugandan traders.

"Shipping containers remain the property of the shipping lines unless purchased with supporting ownership documents,” the embassy said on July 18, 2025.

This misunderstanding has created a costly ripple effect. Shipping lines penalise freight companies for missing containers, resulting in higher container bond fees and increased freight rates, costs that are eventually passed on to South Sudanese traders and consumers. 

Without a dedicated Inland Container Depot (ICD) or dry port in Juba, traders say they have no efficient mechanism to return empty containers.

This logistical gap leads to long turnaround times and higher demurrage and storage costs at Container Freight Stations (CFS) in Mombasa.

Meanwhile, security concerns along the Nimule–Juba corridor, the key overland route linking the Kenyan port to South Sudan’s capital, further compound the problem.

Many Kenyan transporters have reduced trips to Juba due to frequent incidents of banditry and road insecurity.

The Kenya Transporters Association (KTA) recently advised members to avoid moving cargo beyond 4:00 p.m, citing safety risks.

These combined factors drive up transport costs, inflating retail prices of essential goods and straining South Sudan’s fragile economy.

A fact-finding mission by a South Sudanese parliamentary delegation led by Justin Marona uncovered another pressing challenge – the rise of unscrupulous clearing and forwarding agents exploiting importers through arbitrary fees, document manipulation, and unnecessary delays.

Dennis Ombok of Panda Group Logistics noted that many traders lack awareness of customs documentation procedures and clearance timelines, issues that fuel port congestion and inefficiency.

“These lapses result in unnecessary delays and increased port congestion, which further drives up the cost of doing business,” Ombok said.

The delegation, comprising lawmakers, revenue authority officials, and legal advisers, acknowledged the gaps and pledged to push for policy and legislative reforms.

“We are committed to protecting the interests of our traders and will consider any reforms necessary to ease the flow of goods,” said Hon. Marona. He urged stronger partnerships between logistics firms like Panda and institutions such as the South Sudan Chamber of Commerce to enhance trader awareness and compliance.

To restore efficiency along the Mombasa–Juba corridor, stakeholders are prioritising establishment of an Inland Container Depot (ICD) in Juba for faster container turnaround and enhanced border security along the Nimule–Juba corridor to improve transporter confidence.

Others include a crackdown on rogue clearing agents to protect traders from exploitation, continuous training and sensitisation of importers on documentation, timelines, and compliance and deployment of a real-time cargo tracking system to increase transparency and predictability.

As the South Sudanese delegation concluded its visit, Marona reaffirmed the country’s commitment to reforms that would secure smoother trade with Kenya.

“We return to Juba with renewed resolve. Mombasa remains our gateway to the world. We must do everything in our power, through partnerships, reforms, and infrastructure, to keep that gate open and efficient," he said.

In a related development, trade between Kenya and South Sudan is set for a major lift following the recent launch of Trade Facilitation Centres in Kainuk, Lodwar, and Kakuma by the Kenya Revenue Authority (KRA).

These centres, part of the LAPSSET Corridor Program, aim to streamline cargo movements, enhance compliance, and open up business opportunities along the Northern Corridor, which connects Kenya to South Sudan, Ethiopia, and Uganda.

KRA Commissioner General Humphrey Wattanga hailed the initiative as a transformative leap for regional commerce.

“These facilities are a game-changer for trade across East Africa. By bringing KRA services closer to the people, we are securing seamless movement of goods along the South Sudan link road,” he said.

Dr Lilian Nyawanda, Commissioner for Customs and Border Control, emphasised that the centres will promote legitimate trade and strengthen border security while supporting local communities.

“These hubs will facilitate trade, ensure compliance, and provide direct access for cargo destined for South Sudan,” she noted.

The facilities will also help curb smuggling, cargo theft, and illegal dumping, issues that have long plagued transporters and traders along the corridor.

With the centres in place, KRA expects reduced enforcement costs, faster transit times, and improved revenue collection. The initiative forms part of the Eastern Africa Regional Transport, Trade, and Development Facilitation Project (EARTTDFP), backed by the World Bank, and underscores Kenya’s role as a gateway for commerce across East Africa.