The train was an El Zorro Transport train on a test run as part of a 15-year contract with miner Iluka Resources which starts in September.

V-Line owns the track where the train derailed. V-Line spokesman James Kelly said the derailment blocked the Mellis Road level crossing.

"The first four wagons came off the track and about 100 metres of track was damaged," he said.

The track was being cleared yesterday afternoon. Mr Kelly said V-Line hoped to have the track operating again last night under speed restrictions. He said the cause of the derailment was not yet known.

El Zorro's Victorian operations manager Les Branch said three investigations were underway.

"It has not been proven how the train derailed, but three investigations are underway, one from Public Transport Safety Victoria, one from V-Line and our own internal investigation," Mr Branch said.

"Early suspicions are it was caused by a broken section of rail.

"It is something we didn't want but we will resolve the issue and we anticipate rescheduling the test for the next week or week and a half."

An El Zorro Transport operated train derailed near Raywood last month, disrupting passenger services between Swan Hill and Melbourne.