The SABC reports various operational and technical disruptions resulted in commuters being stranded for hours underground on Thursday morning.
The R20bn Gautrain began operating between Sandton and OR Tambo International Airport in 2010.
The Rosebank-Pretoria line was opened in August this year but various problems like cable theft, flooding, breakdowns and strikes have hampered the service.
“We certainly do recognise that there’s frustration out there among our passengers, believe me we share that frustration. It is a brand new system, we are encountering teething problems as we go,” said Gautrain’s Errol Braithwaite.
The company has meanwhile gone to court to stop the bus strike that has affected 135 buses on Gautrain routes this week.
According to one transport expert, Dr Vaughn Mostert from the University of Johannesburg, the Gautrain has not delivered on its promises and that basic transport services are needed between Pretoria and Johannesburg.