Flooding and landslides in Kenya's coastal region has resulted in delays in delivering cargo to and from the port city of Mombasa, the state-owned rail operator said on Saturday.
Heavy rains followed by flash floods have submerged towns across East Africa, rendering hundreds of thousands of people homeless.
In Kenya, the death toll from the floods stands at at least 46, and is expected to rise.
Floods and a landslide on the railway route between the capital Nairobi and Mombasa has forced Kenya Railways to close all cargo services, it said in a statement.
The railway is also used to move cargo to countries including Rwanda, Uganda and South Sudan.
Kenya Railways said limited passenger services would continue.
Data from the Kenya National Bureau of Statistics showed its standard gauge railway hauled 6 million metric tons of cargo last year, from 5.4 million a year earlier.