Mombasa port hit by worst empty containers pile up as ships delay

Importers at the Port of Mombasa are staring at huge costs as shipping lines impose punitive demurrage charges due to delays in the repatriation of thousands of empty containers.

Currently, the port is battling a severe logistical crisis in managing empty containers, threatening to bring operations at East Africa’s biggest port to a grinding halt.

At the port, yards are clogged, trucks turned into mobile storage units as finger-pointing between shipping lines, Empty Container Depot (ECD) operators, and the Kenya Ports Authority (KPA) continue unabated.

Meanwhile, ten container vessels are anchored offshore awaiting berthing slots, alongside four vessels for transhipment cargo and seven conventional cargo ships.

Stakeholders say the last time Mombasa faced such a dire situation was in 2007, when congestion crippled port services, leading to the introduction of off-port Container Freight Stations (CFS) to ease pressure.

At the heart of this unfolding crisis is a growing accumulation of empty containers that are not being repatriated or processed swiftly enough for return to the shipping lines.

Once importers offload cargo, they are given a grace period of 15 days for local cargo and 30 days for transit cargo to return empty containers to a designated ECD selected by liners.

The ships then schedule the repatriation of these containers to bring other cargo. However, this process has broken down. For almost a month, KPA has failed to resolve the problem despite outcry from transporters and importers.

“Shipping lines are failing to move empty containers out of the country promptly, resulting in a massive backlog that is clogging the entire logistics chain,” said the Kenya Transporters Association (KTA) Chairman Newton Wang’oo.

In a recent letter to the industry regulator, the Kenya Maritime Authority (KMA) Director General, Wang’oo said many depots are overwhelmed by the piling of empty containers.

"Many depots are overwhelmed, lacking not just space but also equipment and systems to handle current volumes. There is chaos, prolonged queues, operational delays, and escalating costs,” he said.

He said container depots are overrun, and trucks are trapped in queues stretching for hours or even days just to return empties, effectively paralysing cargo movement across the country.

We established that aggravating the problem is the insistence by some shipping lines that containers be returned to specific depots, even when those facilities are already full.

This has left transporters stranded indefinitely or compelled to pay bribes to secure entry. KTA said that prioritisation systems at certain depots, which favour containers nearing the end of their free storage period, are opaque and susceptible to corruption, deepening inefficiencies throughout the supply chain.

An ECD operator, speaking anonymously, accused shipping lines of misusing depots, saying Empty Container Depots were never intended to serve as long-term storage yards.

Despite their role in causing the delays, shipping lines continue to charge demurrage fees on empty containers, penalising transporters for circumstances completely outside their control.

KTA argues that the situation should be reversed and that shipping lines should compensate truck owners for idling equipment and lost income.

Shipping lines determine when containers are repatriated to the port, contingent upon ship schedules and available yard space. But with congestion rampant, most are failing to communicate timely pre-advice to ECDs.

Mahadi ECD General Manager Eric Wambua explained that what was once a weekly repatriation cycle now takes up to two weeks.

“Recently, we were advised to return 500 containers. We managed only 60 before being told no more space was available at the port. The remaining containers were shut out as the shipping line departed for its next port of call,” said Wambua.

Operating under strict berthing schedules, KPA often watches helplessly as ships depart with empty slots. “Shipping lines are sailing away with unused space, leaving containers stranded,” Wambua noted.

Although KPA has scaled up its container handling capacity to over 2.2 million Twenty-Foot Equivalent Units (TEUs), supporting infrastructure, especially for managing empty containers, has lagged far behind. KPA itself concedes that current facilities are grossly inadequate.

Presently, only five primary depots serve Mombasa, with a collective capacity of 28,400 TEUs, nowhere near enough to meet current demand.

KTA has sounded the alarm, branding the crisis a deepening operational bottleneck that threatens to paralyse the national logistics chain.

Container depots clustered around Changamwe are exacerbating traffic congestion, creating safety hazards as endless queues of trucks block key highways.

Reliance on traffic police for crowd management is proving unsustainable. Meanwhile, corruption-prone booking systems continue to favour containers nearing their free storage expiry, sidelining operational efficiency for underhand deals.

Insufficient offloading capacity means trucks themselves are forced to serve as mobile storage, intensifying the pressure on Kenya’s logistics ecosystem.

According to KSAA Chief Executive Officer Elijah Mbaru, when faced with port congestion, KPA typically prioritises import cargo clearance over handling empty containers, since port performance metrics emphasise cargo throughput.

Mbaru further blamed the backlog on new regulations mandating container cleaning and inspection at designated depots. Additional charges imposed by the Kenya Plant Health Inspectorate Service (KEPHIS)—Sh2,000 per vessel and Sh500 per container—have only complicated the process.

Kenya’s trade imbalance has worsened matters. The country imports substantially more than it exports, creating a surplus of inbound containers with insufficient outbound shipments to clear the backlog. “We are simply not exporting enough to keep up,” said Mbaru. “And the ECDs have not expanded to meet growing demand.”

Mbaru also pointed to international factors exacerbating the crisis. Ongoing Middle East conflicts have forced shipping lines to reroute vessels around the Cape of Good Hope, extending turnaround times and increasing global demand for containers.

To resolve the crisis, Mbaru recommends expanding holding yards within the port itself and automating container management processes.

He also noted that smaller shipping lines not integrated into KPA’s digital systems face manual processing delays that further cripple efficiency.

Despite the evident chaos, the precise cause of the congestion remains unclear to many industry players. An insider at the port attributes the problem to poor berth planning by KPA, suggesting that current cargo volumes do not justify the scale of the congestion.

KPA was unavailable to respond to requests for independent verification of this allegation by the time of going to the press.