Trains in and out of Johannesburg's Park Station were delayed by up to 90 minutes, Gauteng Metrorail said on Monday.
The delays were due to a damaged operating panel, spokeswoman Lillian Mofokeng said.
Trains could not be remotely operated as a result.
"Metrorail is activating its contingency measures by utilising section managers to manually authorise movement of trains," she said.
"This process is slow comparative to the remote operation."
Technicians were working on the problem.
Sapa