Transnet has declared a force majeure after a cyberattack halted all operations.
Investigators are currently looking into the source of the compromise and the extent of the breach.
The ports and freight-rail company says they are implementing all available measures to limit the impact of the compromise.
Sipho Pityana for Business Unity South Africa says there may be difficulties in meeting some contractual obligations for customers.
He says the group is working on restoring its systems.