The driver of the train that rammed into the back of another stationary train in Pretoria, had a 12-month final written warning for violating safety standards, it was reported on Saturday.
The written warning meant that the driver was removed from driving and re-assigned to other duties, The Citizen reported.
The allegation was made by the National Transport Movement (NTM), a breakaway union from SA Transport and Allied Workers Union, following a statement by the Passenger Rail Agency of SA (Prasa) claiming the union had been linked to the recent torching of trains around the country.
"This driver had to be used because of the strike action," NTM president Ephraim Mphahlele told the newspaper.
"We believe that operations are suffering and they ended up having to use this driver at the last minute."
Mphahlele said the driver had not been driving for the past two years.
At least 200 people were injured, some critically, when the two passenger trains collided near Saulsville in Pretoria on Thursday.
No deaths were reported, but Prasa said two people, including a train driver, sustained critical injuries. Nineteen others suffered serious injuries.
Paramedics examined 350 people, including children, at the scene.
Prasa spokesperson Lawrence Venk would not comment on NTM's allegations.
"We won't comment on the train driver, pending the outcome of [an] investigation, as it is directly in relation to safety issues that are part of the brief of the investigation," he told the newspaper.