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.
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.
A driver is in hospital with a serious head injury after his car was hit by a train at a rural level crossing.