A cargo handling and clearance dispute among South Sudan authorities could slow down the movement of transit goods to and from the land locked country.
The South Sudan Transport Minister and the country’s Commissioner for Customs Services have issued counter directives.
In February Kenya granted a request by South Sudan's Transport minister Madut Biar that the country's cargo from the port of Mombasa to pass through the privately owned Nairobi Freight Terminal.
This was meant to cut the distance from Mombasa to Juba by 489 kilometres.
Kenya's Transport Cabinet Secretary further welcomed the idea of South Sudan bound cargo going through the Naivasha Inland Container Depot and onward to the Malaba.
Following the clearance, South Sudan Commissioner for Customs Service Division Lilian Nyawanda on April 25 published a list of six companies authorised clear the country's cargo at the Nairobi Freight Terminal.
However, in a counter directive, South Sudan Ministry of Trade and Industry wrote to its Kenyan counterpart asking CS Betty Maina reversing the commissioner’s order.
The S.Sudan trade minister said the commissioner had acted unilaterally hence her directive was null and void.
"The government of South Sudan is in process of acquiring the land Title Deed of the Naivasha land designated for South Sudan Inland Container Depot, therefore our goods will remain in Mombasa until the Naivasha project is developed, for storage," Kuol Athian Mawien said in the letter dated May 23.
The standoff is gradually affecting South Sudan importers who have raised concern over slowed down business due to the confusion.
Through their representatives in Kenya, the Kenya International Freight and Warehousing Association (Kifwa) cargo owners called for public consultation to end the back and forth that has already led to supply delays.
Kifwa chairman Roy Mwanthi said members are demanding for a clarification from Kenya Ports Authority on which circular it is implementing between the S. Sudan commissioner's and the ministry of trade.
He warned that further delays could cause cargo pile up at the Port of Mombasa as owners wait the way forward.
South Sudan is second after Uganda on the use of the Mombasa port, accounting for 9.9 per cent of total transit volumes.
Uganda accounts for the lion share of 83.2 per cent while DR Congo, Tanzania and Rwanda account for 7.2 per cent, 3.2 per cent and 2.4 per cent, respectively.
