Two men have been killed after being struck by a train at Altona Meadows in Melbourne's south-west.

Key points: Train driver is being looked after

Train driver is being looked after Police unsure why the pair was on the tracks

Police unsure why the pair was on the tracks Trains delayed on Werribee Line

Police believe the men were on the tracks near the intersection of Merton Street and Railway Avenue when they were hit by a city-bound passenger train shortly before midnight.

Inspector John Kearney said the train driver spotted the men but was unable to stop.

"He's getting looked after," he said.

"We do know that he applied his emergency brakes and attempted to avoid the collision but unfortunately he was unable to.

Locals said people often crossed the tracks where the men were hit. ( ABC News: James Hancock )

"We've got some specialist services coming down to examine the scene. Once they've done that, the bodies will be removed and [be] subject to a post-mortem."

Locals said many people took a shortcut across the tracks even though there was a pedestrian bridge about 500 metres away.

"I've known people to go to the local gym [and] go across the tracks there to get access to Laverton. What I can't understand is how they didn't know a train was coming," one local said.

Victoria Police's transport crime unit is investigating the incident.

Detective Sergeant Alistair Boyd said the investigation was still in its early stages.

"At this stage, early indications are [that] the circumstances are not suspicious," he said.

"It is unknown what the two males were doing in the area at the time."

The two men have not been formally identified.

Metro Trains said there were 13 passengers on the train at the time.

Trains were suspended between Laverton and Westona after the incident, but services have since resumed.