Emergency services worked for 20 minutes to free 12 trapped passengers and the driver aboard the train.
The passenger train was heading north at Roxburgh Park, about 500 metres south of Craigieburn railway station when crews were called.
It is believed the Apex quarry freight train was travelling at three to four km/h while the passenger train was travelling at normal speed.
Some passengers had to be carried out of the train and three people sustained serious injuries while the driver received a cut to his head.
The two occupants of the Apex freight train were uninjured.
Police last night said officers at the scene had questioned the driver and he was to undergo blood and alcohol testing.
Victorian Transport Minister Martin Pakula has said it is too early to speculate on what had caused the incident.
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