Shipping containers were sent tumbling when a 1.7 kilometre-long train with 55 carriages derailed near Inverleigh early on Monday.
Sixteen of the carriages went off the tracks, blocking the rail corridor between Adelaide and Melbourne.
No one was injured and the cause is under investigation.
"We know there was heavy rainfall and some flash flooding in that area but at this stage it's too early to know what the cause was of the train derailment," Victoria State Emergency Service Chief Officer Tim Wiebusch told reporters on Monday.
"We are lucky we weren't dealing with a passenger train in this instance and that the crew on board that freight train were also unscathed."
Mr Wiebusch said authorities were working out how to get heavy machinery to the rural area and it could take more than a week for the debris to be cleared.
The Australian Transport Safety Bureau has taken control of the site.
"Investigators will survey the site and collect any relevant components for further examination and analysis," bureau chief commissioner Angus Mitchell said.
"They will also obtain and review any recorded data, weather information, witness reports, and relevant train and track operator records."
