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"At 5.30am the system had failed," said spokesman Solomon Makgale.
He explained that the air traffic and navigation services company had a problem with the system in the early hours of the morning before the system failed.
The system was up again by 6.30am but the one hour lost in processing traffic through the busy aviation hub, meant domestic flights would experience delays at the airport for the rest of Thursday.
The problem only affected domestic flights at that airport.
Makgale advised travellers to phone the airline they had booked with to establish their new travel times.
Sapa