The congestion, now in its third day, has turned one of East Africa's busiest border posts into a major bottleneck, leaving the Ugandan side unusually quiet as only a handful of trucks manage to cross each day.
Drivers say the revised cargo clearance procedure has significantly slowed movement.
Previously, cargo was fitted with an electronic tracking seal at the point of loading. Under the reinstated system, however, every truck must also be fitted with a metallic electronic seal at the border before entering Uganda, increasing the processing time for each vehicle.
The delays have left hundreds of drivers stranded along the highway, exposing them to insecurity and poor living conditions without adequate access to food, sanitation facilities or safe places to rest.
"We have nowhere to eat, nowhere to sleep, and nowhere to help ourselves. We are suffering," said truck driver Samuel Njoroke.
Another driver, Yusuf Hadith, warned that fatigue caused by the long delays is increasing the risk of road crashes.
"We are not sleeping and that is becoming very dangerous on the road," he said.
Transporters say the congestion is also imposing heavy financial losses, with trucks consuming more fuel than planned while perishable goods worth millions of shillings risk spoiling before reaching their destinations.
Abel Namenge of the Kenya Long Distance Truck Drivers Union said some stranded drivers have also fallen victim to criminals.
"Some of us are transporting goods that are ready for the market. We are being attacked on the road and our cargo stolen. We have nowhere to eat, yet we are also human beings," he said.
Clearing agents say the additional sealing requirement has cut their daily processing capacity by more than half.
Chrispinus Omuse of the Kenya International Freight and Warehousing Association (KIFWA) said the number of trucks cleared each day has dropped from between 1,500 and 1,600 to about 750.
Responding to the complaints, URA Eastern Region Manager Abbey Mawerere defended the reinstatement of the metallic cargo seals, saying the measure was introduced to curb a rise in cargo theft after the seals had been temporarily suspended.
"We discovered that during the period when metallic cargo seals had been suspended, some dishonest individuals started stealing cargo. That is why we decided to resume sealing every truck," Mawerere said.
He acknowledged the disruption caused by the long queues but said URA staff were working around the clock to clear the backlog and restore normal operations by tomorrow.
However, transporters and clearing agents rejected the assurance, calling for the immediate suspension of the directive.
Peter Sireka, chairperson of the Uganda Clearing Industry and Forwarding Association (UCIFA), criticised the implementation of the policy without adequate consultation.
"We want this directive suspended. Such decisions should not be implemented from the head office without first assessing the situation on the ground," he said.
Simon Okwi of the Kenya Transporters Association (KTA) warned that transporters could suspend operations if the matter is not resolved within the next two to three days.
"We are giving them only two to three days. If nothing changes, we shall mobilize our drivers to stop working. This cannot continue in Uganda," he said.
The standoff threatens to disrupt trade along the Northern Corridor, East Africa's principal transport route linking the Port of Mombasa to Uganda, Rwanda, South Sudan, eastern Democratic Republic of Congo and other landlocked countries.