"Transnet Freight Rail confirms that urgent recovery efforts are underway to restore operations to its ore corridor," it said.
The line stretches 861 km from iron ore mines at Sishen in the Northern Cape to the Saldanha port in the Western Cape.
The derailment took early on Wednesday, Transnet said in a statement.
A shortage of locomotives and spares, as well as cable theft and other vandalism of its infrastructure is hampering the state-owned freight rail operator's efforts to haul minerals and other commodities to ports.
Miners say Transnet's problems continue to cost them billions of rand in lost export revenue.
In recent weeks, both the iron ore and coal export lines have suffered derailments which halted train operations for days.
Heavy rains also impacted Transnet operations at the beginning of the year.