Fourteen carriages from the middle of the Pacific National train derailed about 1am on the O'Tooles Road level crossing.

About 500 metres of the track has been damaged with a quarter of the 200,000 tons of grain being carried spilt. 

Pyramid Hill Leading Senior Constable Jason Brady said a track fault appeared to be the cause and that the drivers had escaped uninjured.

"The two drivers were shaken but not stirred," he said.

Leading Senior Constable Brady said he was surprised more carriages hadn't overturned and that it was lucky it wasn't a passenger train.

"If it was a morning V/Line passenger train it could have been a whole different story with a much more dire outcome," he said.

The cargo was being taken to Melbourne but GrainCorp spokesman Angus Trigg said it wasn't clear who's grain was on the train. 

"The train is a Pacific National train but it’s possible it could be leased by someone else," he said. 

"We're not sure if its us. We're out sending a team to have a look so we'll have to wait and see." 

It's believed it will take up to nine days to salvage the wreck and repair the track.

A V/Line spokesperson said buses would replace trains between Swan Hill and Bendigo in the meantime.

Public Transport Victoria will investigate the cause of the accident.