"Heavy rains have caused severe disruptions in the North East Corridor. Our teams are out in full force and assessing the damage to the rail line," Transnet said in a brief statement. The state-owned firm did not provide more detail, but said it would provide further information during the day.
The North East Corridor links South Africa to Swaziland, Zimbabwe, Mozambique, Zambia and the Democratic Republic of Congo, according to the Transnet website.
South Africa's rail system is an important element of its economic system, moving the nation's goods to buyers in other countries.
Hampered rail efficiency, like electrical shortages, have had an impact on the nation's output and GDP according to analysts.