The accident happened as the city-bound train was approaching the Bonbeach railway station just before 6:30am (AEST).
The truck driver suffered minor injuries and the construction materials on the truck spilled on to the road.
No-one on the train was hurt.
Sergeant Herb Lonsing, from the Moorabbin highway patrol, says it is lucky there were no serious injuries.
"We're very fortunate the driver received very minor injuries. He's walking and talking to the police," he said.
"He's helping with (our) enquiries and we're just grateful nobody else was seriously injured and the passengers in the train are fine."
Sergeant Lonsing says the investigation into what happened is still underway.
"The tray was exposed over the railway line," he said.
"It could've been a tragedy again. These crossings are dangerous and people do need to take care on these crossings.
"Just don't cross over where those yellow lines are."
Train operator Metro says the Frankston line has been reopened and delays of about half an hour are expected.
Buses will be used to help clear the backlog of commuters.