Victoria Police say it is understood the truck became stuck on a level crossing.
The incident happened at Station Street in North Shore just after midday on Monday.
The driver died at the scene and has not yet been formally identified.
About 25 passengers onboard the V/Line train were evacuated but no one else was hurt.
There were major delays on the Geelong and Warrnambool lines after the collision, with trains running between Southern Cross and Lara but replaced by coaches between Lara and Waurn Ponds.
Further service changes and significant delays were expected on Monday afternoon and evening, with V/Line urging passengers to check its website, app or social media for updates.
"We extend our thoughts to those affected by this tragic incident, and we thank passengers for their patience while we work to get them to their destination as quickly and safely as possible," a V/Line spokesman said.
"We will provide the driver and our workers with the necessary support during this difficult time."
Circumstances surrounding the collision are still under investigation.
The Australian Transport Safety Bureau was gathering further information about the incident on Monday afternoon.
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