A ‘critical incident’ was declared yesterday following the collision in Fisherton Tunnel close to London Road, Salisbury.
It happened when a carriage was derailed after hitting an object, and a second train then crashed into it when signalling was damaged.
One of the trains involved was the 1708 Great Western Railway (GWR) service from Portsmouth Harbour to Bristol Temple Mead.
The crash happened at around 6.45pm yesterday.
It was first reported that only minor injuries had been suffered as a result of the crash.
However, British Transport Police (BTP) have now said that a train driver has suffered ‘life-changing’ injuries.
A statement reads: ‘Thirteen people were taken to hospital by ambulance, where they have received treatment for minor injuries. One remains there.
‘Unfortunately, the driver of the train was more seriously injured and his injuries are believed to be life-changing.
‘He also remains in hospital in a stable condition this morning, and his family have been informed.’
Disruption following the crash is expected to last for several days.
GWR services between Portsmouth and Cardiff will be affected.
Passengers are urged not to travel on the affected parts of the network.
Martin Frobisher, Network Rail’s safety and engineering director, said passengers ‘must have had a really scary experience, and we’re very sorry for that’.
He told BBC Radio 4’s Today programme: ‘We’re obviously starting now a very detailed and forensic investigation into what happened.
‘The Rail Accident Investigation Branch (RAIB) are on site and they’re incredibly thorough in the work that they do.
‘And that’ll help us learn from this, and that’s why these events are very rare, because we follow it up very, very carefully, and make sure that we do everything possible to prevent it for the future.’