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Network Rail is investigating whether it had been asked for permission to open a gate at a level crossing before a vehicle was hit by a train.
A man, aged in his 40s, suffered a severe head injury in the collision on the line between Cambridge and Ely on Friday afternoon.
He was airlifted to Addenbrooke's Hospital but his injuries are not thought to be life threatening.
The level crossing between Ely and Waterbeach in Cambridgeshire is used by fewer than 10 vehicles each day, Network Rail said, and is "user-worked".
Spokesman Ross Easton said there are "clear instructions" telling people to phone a signaller, based in Cambridge, to ask for permission to cross.
When they are given the all-clear users manually open the gates and are asked to call the signaller again when they have crossed.
Mr Easton confirmed the rail operator is looking into whether a call was received before the incident involving the 1354 Great Northern Kings Lynn - London King's Cross service.
A train has hit a vehicle on the line between Cambridge and Ely with paramedics treating a man in his 40s for a severe head injury, the East of England Ambulance Service has said.
A spokesman said an emergency call was received at 2.34pm on Friday with the East Anglian Air ambulance, a land ambulance, three ambulance officers, the hazardous area response team and police sent to the scene near Stretham in Cambridgeshire.
One patient, a man in his 40s, has been taken to Addenbrooke's Hospital in Cambridge for treatment.
A British Transport Police spokesman confirmed officers were on the railway line between Cambridge and Ely after reports a train had struck a vehicle on a level crossing.
Police were alerted just after 2.30pm.
The spokesman added that officers were being supported by the ambulance service.
Network Rail spokesman Ross Easton said: "At around 2.30pm, the 1354 Great Northern Kings Lynn - London King's Cross train struck a vehicle at a level crossing between Ely and Waterbeach in Cambridgeshire.
"A man has been airlifted to hospital but his injuries are not thought to be life threatening.
"This type of level crossing is typically used by fewer than ten vehicles per day and requires users to telephone a signal box for permission to cross. We are assisting the emergency services at the scene."
Latest ITV News reports
Network Rail has confirmed a level crossing where a train hit a car on Friday is one of those earmarked for closure.
The driver of a car that was struck by a train in Cambridgeshire did not have permission to be on the level crossing where it was hit.