Detective Sergeant Alistair Boyd ruled out suspicious circumstances, and suggestions the men had jumped onto the tracks from a nearby bridge, a regular graffiti target. He also said there were no cans of spray paint found near the bodies.
Describing the scene as a “definite tragedy”, Det Sgt Boyd said the driver had seen the men and applied the emergency brakes as quickly as he could.
But the driver could not prevent the deaths.
“Trains are a large object and they’re deadly – train tracks are a very dangerous place,” the detective told reporters.
The traumatised train driver was undergoing counselling on Friday, Metro spokeswoman Sammie Black said.
“Unlike a car, our drivers are unable to swerve the train or bring it to a stop quickly and these incidents can have a traumatic effect on our drivers,” Ms Black told AAP.
Two grief stricken women, believed to be family members of the deceased, went to the scene just before 11am on Friday.
They were consoled by detectives before being taken away in an unmarked police car.
Detectives are investigating whether an abandoned car found nearby belonged to the men, or if they were known to each other.
Nearby residents say a number of people have died on the same stretch of track, which is not fenced off and often used as a crossing by pedestrians.
The deaths occurred on a straight part of track where trains can be seen and heard coming from a distance. The train involved was travelling within the 65km/h speed limit, police say.