Kenyan importers have told Reuters news agency they have been forced by the Kenya Port Authority (KPA) to use a new rail line between the coastal city of Mombasa and the capital Nairobi.
The port confirmed the policy in August, but rescinded the order in October after protests, Reuters reports.
Businesses told the news agency that little has changed and they are still required to use the more expensive railway.
They say their costs have shot up nearly 50% thanks to extra fees, the longer time it takes to clear goods at the congested Nairobi train depot and because they have to send lorries to collect the goods from there.
Importers must pay at least 25,000 Kenyan shillings ($243; £188) for a truck to collect the goods from the Nairobi depot and 15,000 shillings in depot fees, three businessmen, who asked not to be named, told Reuters.
The higher charges are necessary to meet loan repayments, Daniel Manduku, head of the state-run KPA and a board member of Kenya Railways, said, the news agency reports.
The contract between China's Exim Bank, KPA and Kenya Railways requires KPA to provide one million tonnes of cargo to the railway per year, according to Reuters.
Kenya owes Exim Bank 660 billion shillings for the railway and other projects, about a tenth of its total national debt. The bank and KPA did not immediately respond to Reuters' request for comment.