All transit cargo destined for Uganda, Rwanda and South Sudan ill now be transported via the SGR to Naivasha Inland Container Depot (ICD).
Alternatively, other cargo will be transported through the Metre Gauge Railway to Tororo or Kampala, Uganda from next month.
The government plans to make the Naivasha ICD centre for cargo destined for landlocked East African countries.
In a statement seen by Pulselive.co.ke on Friday, Transport CS James Macharia said that EAC Presidents made the decision following the coronavirus pandemic.
Macharia says all transit cargo railed to ICD Naivasha will then be collected by trucks to the partner states via Busia or Malaba.
"... in recognition of the need to contain the spread of Covid-19 pandemic within the region, have considered appropriate cross border transportation modalities to reduce human traffic movement," the statement read in part.
The time for transporting cargo from Mombasa to the Naivasha ICD will also be shorter compared to using trucks.
The Naivasha ICD will also reduce congestion in the Nairobi ICD and Mombasa port.
He further, said the fuel products will be transported by pipeline to Kisumu and thereafter by lake Victoria to Port Bell or Jinja.