Wangaratta police Acting Sergeant Scott Mundie said the woman’s SUV was on the train tracks at Katunga when it was hit by the oncoming freight train shortly after 5pm.
He said the train was travelling at about 60km/h at the time of the collision.
The crossing at Allerts Rd does not have boom gates, and only has flashing lights installed, Act Sgt Mundie said.
Police are still investigating how the vehicle came to be on the train tracks, and were unsure at this stage whether the woman tried to drive across the crossing or whether it was just stopped on the tracks, Act Sgt Mundie said.
The driver and sole occupant of the SUV — a 62-year-old Katunga woman — was injured in the incident and was flown to Melbourne’s The Alfred hospital in a critical condition.
She remained in hospital in a critical condition on Wednesday afternoon.
No-one else was injured in the crash.
Cobram and Numurkah SES crews, as well as police, ambulance and fire brigade crews, attended the crash.
The freight train was not derailed in the incident.
The exact circumstances surrounding the collision are yet to be determined and investigations remain ongoing.
Anyone who witnessed the crash or saw anything leading up to it is asked to contact Crime Stoppers on 1800 333 000 or www.crimestoppersvic.com.au