The affected stations were Sandton, Midrand, Langlaagte and Loveday Street in the Johannesburg inner city, said Superintendent Wayne Minnaar.
They had been closed since 9.30am.
"The eNaTIS licensing system may be offline in certain areas. However, in the inner city, staff are attending a union meeting," he said.
Minnaar could not confirm when the system would be running again, but said technicians were dealing with the problem.
The system, which links vehicle and driver records with police, financing and insurance data, has crashed a number of times since its implementation in 2007.
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