Investigators have begun sifting through the wreckage of a Sydney-to-Melbourne train that derailed last night, killing two people and injuring 12 others.

Key points: The train's driver and pilot were killed on impact

The train's driver and pilot were killed on impact Police said it was a "miracle" most of the passengers only had minor injuries

Police said it was a "miracle" most of the passengers only had minor injuries An initial investigation into the cause of the crash could take days

The XPT train, which was carrying 160 passengers, was travelling from Sydney to Melbourne when it derailed at Wallan shortly before 8:00pm.

The impact killed the train's driver, a 54-year-old ACT man, and the train pilot, a 49-year-old Castlemaine man, Victoria Police confirmed this morning.

Passengers described luggage flying through the air as the train came off the tracks.

One passenger was taken to the Royal Melbourne Hospital with upper body injuries. Another eight people were taken to the Northern Hospital with minor injuries.

Three others were also taken to Kilmore hospital with minor injuries.

The train was on its way from Sydney to Melbourne. ( Twitter: @Rickard_Scott )

V/Line had reported track faults in the days leading up to the accident.

Acting Inspector Peter Fusinato said Victoria Police would be working with the National Rail Safety Regulator and the Australian Transport Safety Bureau to determine what caused the crash.

"Obviously we've still got a major crime scene there, we've still got two deceased that we need to remove," he said.

"That'll be our main focus, humanely looking after them as best we can."

The initial investigation will take days and must be completed before the wreckage can be cleared.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 36 seconds 36 s The XPT service left Sydney yesterday morning, and was running two hours behind schedule when the crash happened just before 8:00pm.

The derailment left the train's engine and first carriage on its side.

The tracks were also damaged in the derailment.

"It would have been looking like a horrific scene," Acting Inspector Fusinato said, adding it was a "miracle" that most of the passenger injuries were minor.

"I've just been down and walked the scene and yeah I'm very surprised that there weren't more serious injuries.

"We're very fortunate in that regard."

'People started moving around, luggage went flying'

Scott Rickard, who was in the second carriage of the train, described it coming to a sudden stop.

"Stuff flew off our tables, people started moving around, luggage went flying, that kind of thing," she said.

"Our carriage finished on an angle."

The train was carrying 160 passengers. ( Storyful: Richard Sherman )

Dr Rickard said she was stuck on the train for about 10 minutes after it derailed.

"There were people lying all over the place and we had to kind of make sure people weren't injured," she said.

Most of the train's passengers escaped with only minor injuries. ( Supplied )

Many passengers were able to make their way to a nearby service station, which was set up as a triage area.

But police said there were still more than a dozen people who remained unaccounted for, possibly because they had left the scene without speaking to emergency services.

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"We just ask those people if they could to contact Crime Stoppers and provide us with their details so we can mark them off," Acting Inspector Fusinato said.

"And anyone who may have booked a ticket as well, if they didn't take the train, we'd like to hear from them as well via Crime Stoppers just so that we can make sure we've covered off everyone."

The passengers were transferred to Melbourne in coaches.

Ongoing track faults in lead-up to derailment

Leyon Gray, who was travelling from Sydney, said the train crew told passengers there had been an ongoing signalling problem that they had reported.

"They said we could be there for half an hour because the signals were malfunctioning," he said.

"And the train got going and we were probably doing 80 or 90 [kilometres] an hour.

"Next thing we were thrown out of our seats. The whole train derailed.

"Bits of track and sleepers going everywhere. The entire train with the exception of the rear locomotive was totally derailed."

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V/Line had reported several delays between Albury and Southern Cross stations in recent days due to an "ongoing track fault".

Shortly after 4:00pm yesterday, the Seymour V/Line Twitter account said the 12:45 Albury to Southern Cross service would be delayed by approximately 70 minutes due to an "ongoing rail equipment fault near Wallan".

The president of the Rail Futures Institute, John Hearsch, told AM a fire at a signalling facility close to the accident site had recently affected signalling between Donnybrook and Kilmore East.

"So I'm sure the ATSB [Australian Transport Safety Bureau] will be looking very closely at that to see whether there's a link between the signalling problems, the set of points at the entrance to the crossing loop and the accident," Mr Hearsch said.

'You just hang on for grim death'

A Sydney couple who were on their way to visit their son in Melbourne said the crash and its aftermath were terrifying. They've cancelled their return trip.

"You just hang on for grim death. You're being thrown around, the thing's going along tilting over and all you can look out the window and just see dirt and debris and stuff flying up past the windows and the track itself is just twisted and bent," the man said.

"It probably went about 150 metres before it stopped, there were carriages going sideways — pretty horrifying."

Paramedics triaged and assessed the passengers following the incident. ( ABC News )

The woman said her thoughts were with those who had died.

"We're very sad about that. Two people who went off to work this morning and never went home," she said.

Widespread delays

The Victorian Department of Transport said services on the Seymour, Shepparton and Albury lines would be affected by the incident today while services on some other lines were expected to be cancelled due to ongoing industrial action.

"Passengers should check the V/Line website or app for the most up to date information before they travel," the department said in a statement.

A joint statement from the Victorian, NSW and Federal governments said they were working closely to support all those involved in the incident.

"A range of support measures will be available to passengers, crew and their families," the statement said.

"The Australian Transport Safety Bureau and the Office of the National Rail Safety Regulator will conduct a full and thorough investigation to establish the cause of the incident."

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