Metro, Public Transport Safety Victoria and the Chief Investigator's Office will investigate the cause of the crash.

Advanced life support paramedics from Craigieburn, Hadfield, Oak Park, South Morang and Whittlesea and intensive care paramedics were called after the accident about 8.30pm on Tuesday.

Paramedic Stephen Moody said when crews arrived a number of injured passengers were still on the train.

"Paramedics spread out across the first two carriages and next to the tracks to assess a total of 15 people. Five of them required hospital treatment."

They included:

■A 15-year-old-girl, who was taken to the Royal Children's Hospital with suspected spinal injuries after falling from her seat.

■The passenger train driver, a 45-year-old man, who was taken to the Royal Melbourne Hospital with a head cut. It's believed he may have briefly lost consciousness.

■A 22-year-old woman was taken to the Royal Melbourne with cuts to a leg.

■A 22-year-old-man was taken to the Royal Melbourne with chest pain after he was thrown against a seat.

■A 39-year-old woman was taken to the Northern Hospital at Epping with chest pain. She had a suspected broken chest bone and bruising.

Mr Moody said all involved were shaken and distressed but were out of the carriages within about 20 minutes.

"The passenger train's driver was the last patient to leave the scene. He wanted to make sure all those on board were being looked after."

Metro spokesman Chris Whitfield confirmed the train was involved in the Holmesglen collision, but added it had been stationary then.

"It's a coincidence. In that case the train was the one that was hit and in this case, this train has hit the other."

Mr Whitfield said the train was running to schedule. However, investigations would continue. The driver had 20years' experience.

Public Transport Safety Victoria CEO Allan Osbourne said he and Chief Investigator Ian McCallum would collate data on signalling, infrastructure and brakes.