12.45 UPDATE: Ambulance Victoria has confirmed four people were assessed by paramedics following Saturday night's incident, but only one person was transported to hospital.
A man aged in his 40s was taken to Ballarat Base Hospital with head, leg and back injuries in a serious but stable condition.
EARLIER: Two men have been taken to hospital after a V/Line train struck a closed level crossing in Ballarat overnight.
The incident occurred just after 11.30pm on Saturday with the 10.16pm Southern Cross to Wendouree train failing to stop at the Ballarat Railway Station and hitting the gate at Lydiard Street North.
The driver and passenger suffered minor injuries and were taken to hospital for observation.
A conductor and another passenger who were the only other people on the train were treated at the scene, with one taken to hospital for further observation and treatment.
Services did not operate beyond Bacchus Marsh following the incident, with alternative transport provided.
The Road Safety Transport Authority is investigating the cause of the crash.
In a statement provided to Radio Ballarat, V/Line has confirmed trains are running on Sunday through the area with traffic management in place.
"The safety of our staff and passengers remains our first priority and an external investigation by the relevant authorities will be undertaken," a spokesperson said.
Pictures: The damaged level crossing on Sunday [J Fitzgibbon/Radio Ballarat]