The truck driver died after his vehicle crashed into the V/Line train near Barwon Terrace in South Geelong at 6.40am on Monday.
The injured driver was freed from the wreckage by firefighters and treated by paramedics, but died at the scene.
It appeared the truck had gone past the level crossing boom gates and the train was not able to stop in time, Acting Senior Sergeant Fletcher Pearson.
The train driver was not injured although he was left shaken.
"It's not a good scenario," Acting Senior Sergeant Pearson told media at the scene.
"He's come to work. He's doing nothing wrong. He's driving down and we've got a truck that, for some reason, has turned on the train tracks in front of him."
No passengers were onboard the service, which had been heading towards Waurn Ponds and was due to travel to Melbourne.
Damage to the train appeared to be limited to a broken light and a scrape on one carriage.
Coaches replaced Geelong and Warrnambool V/Line services through the area on Monday morning but normal train services resumed about 1.30pm.
The section of train line that was closed carries more than 110 journeys each weekday.
The Australian Transport Safety Bureau is investigating the crash, with workers already on site to examine the railway infrastructure, truck and other evidence.
"Should any critical safety issues be identified at any stage during the course of the investigation, the ATSB will immediately notify relevant parties so appropriate safety action can be taken," a spokesman said.
Anyone who saw what happened has been urged to contact police.
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