The exact circumstances of the crash in Rafz in the canton of Zurich remain under investigation, said SBB in a statement, while stressing that safety is a top priority for the state-owned rail operator.
As a precautionary measure, it said reduced speed limits have been introduced in the approach to the traffic signal.
The S-Bahn 18014 left platform 4 of the Rafz station at 6.40am and travelled toward Schaffhausen, despite the stop signal.
The emergency brake of the train was activated as the train was travelling at 59 kilometres an hour and it came to a halt 100 metres past the the signal.
A few seconds later, an InterRegio train 2858 travelling from Zurich at a speed of 110 km/h struck the regional train laterally.
SBB said the InterRegio train was travelling on track 5 instead of track 3 because of a delay.
The InterRegio train derailed and the carriages were significantly damaged while 60 metres of track had to be replaced.
According to initial estimates, the damage estimate amounts to “several million Swiss francs”.
The driver of the InterRegio was seriously injured, an apprentice driver was less seriously injured and four passengers were slightly hurt in the collision.
After checks and treatment, the passengers were able to leave hospital the same day, SBB said.
The InterRegio driver’s life is no longer in danger following surgery, but he remains in intensive care, it said.
At a press conference, the head of SBB Andreas Meyer refused to comment on why the driver of the InterRegio ignored the stop signal, saying that the inquiry into what happened is still ongoing.
The prosecutor’s office for the canton of Zurich and the federal government’s accident investigation authority are investigating the accident.