Train services between Pretoria and Johannesburg have been severely affected due to sinkholes, Metrorail said in a statement on Thursday.
It has affected the route between Irene and Olifantsfontein.
"The heavy rain has caused the soil under the rail tracks to sink to dangerously low levels rendering the soil unstable," it said.
Metrorail said both the up and down mainlines between Irene and Olifantsfontein would be closed. Instead, a shuttle would run from Pretoria to Centurion and from Olifantsfontein to Johannesburg.
Buses would also supplement the train services between Centurion and Olifantsfontein.
Metrorail said its technical teams were working to restore the service.