The crash happened about 7pm when a city-bound Metro train stopped unexpectedly at a level crossing on Maidstone Street, Altona.

A V/Line train coming from Geelong then rear-ended the Metro train at low-speed.

About 60 people were assessed by Ambulance Victoria paramedics, with four people being taken to hospital and seven treated at the scene.

There were no passengers on the Geelong train, but the driver and conductor received minor injuries.

A Public Transport Victoria spokeswoman said the trains were removed from the tracks about 2pm on Saturday and the tracks were cleared completely about 5pm.

V/Line and Metro officials then inspected the section of track and signals before declaring it safe, the spokeswoman said.

The first V/Line train from Geelong to Melbourne departed at 12.21pm on Sunday, with a Geelong-bound service departing at 1pm.

Metro services on the Werribee line, which had been diverting through the Altona loop, have also resumed their normal route.

The Office of the National Rail Safety Regulator and the Transport Safety chief investigator's office both investigated the crash scene.

Police are believed to be investigating reports that vandals had attempted to stop the train in order to launch a graffiti attack.