When paramedics arrived on the scene, they found carriages from both trains tilting half off the track.
The two trains smashed into eachother in Pretoria, the capital.
Metrorail said more people are still believed to be trapped inside the two trains which collided in Mountain View, northeast of Pretoria, on Tuesday.
So far three people have been declared dead and two are reportedly critically injured.
"On the scene of this morning's train accident at the Mountain View Station".
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"Most unfortunately as a result of the collision and the impact, we had three fatalities from this accident and more than 300 people that were seen by emergency services, ' Mofokeng told News24".
According to reports there were 800 people on board at the time of the crash.
Masha said police had opened an inquest docket to investigate the cause of the collision. Some victims are still being freed from the trains, whereas others have been rushed to local hospitals after initially receiving treatment on the station's platform.
Tshwane Mayor Solly Msimanga said he has always raised concerns about the infrastructure of railway lines and their outdated resources. "We can not lose any more lives, there needs to be some kind of upgrade in terms of signalling that is in here".