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Images showed a fire engulfing several passenger carriages that were derailed at the scene near Kroonstad, 200 kilometres (125 miles) southwest of Johannesburg.
“The death toll has increased to 12,” provincial government health spokesman Mondli Mvambi told AFP, adding that at least 180 people had been injured, two of them critically.
“It is feared that they could find more bodies as the search, recovery and rescue work is ongoing,” Mvambi said.
Medics gave earlier gave a toll of four people killed.
Black smoke poured from carriages lying on their side close to a road.
Speaking on the phone from the scene of the accident, rail company official Leboho Mokhalipha told AFP that teams were digging through the wreckage in search of any passengers trapped inside.
“There are still some people inside the coaches — the ones that were on fire,” said Mokhalipha.
Some victims were treated at the scene while others were taken to hospital, local media reported, as uninjured passengers walked away from the wreckage, many carrying their luggage.
The New Year is a busy period for transport in South Africa, with railways and roads carrying passengers returning to work after the holidays.
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