Transnet, operates nearly three quarters of all Africa's rail network and most of the ports in Africa's most industrialised economy, said its processes were all above board.

"The Commission's investigation emanates from information indicating that the South African Port charges are much higher than the global average," the watchdog said.

Transnet, which reported a slight rise in full-year revenue due to an increase in railed cargo, said in a statement that it would cooperate fully with the inquiry.

"Transnet is comfortable and confident that its processes are fair, just and in line with relevant legal requirements," the company said in a statement.