The direction of rail tracks at the site of a fatal train derailment north of Melbourne on Thursday were changed earlier that day for the first time in weeks, the ABC has been told.

Key points: The Rail, Tram and Bus Union said the track had been awaiting maintenance

The Rail, Tram and Bus Union said the track had been awaiting maintenance The cause of the crash is being investigated by the Australian Transport Safety Bureau

The cause of the crash is being investigated by the Australian Transport Safety Bureau It comes as state MP Steph Ryan said she had held "significant concerns" about the line for years

The Sydney-to-Melbourne XPT service, which was carrying 153 passengers, derailed at Wallan shortly before 8:00pm.

The train's driver, 54-year-old Canberra man John Kennedy, and a train pilot, a 49-year-old Castlemaine man, were killed and 11 passengers were taken to hospital with minor injuries.

The crash happened about 1.5 kilometres north of Wallan station, near a set of points where one track diverged into two, otherwise known as a turnout.

Trains had been going straight through the turnout for two weeks, but on Thursday were diverted around through a track loop at Wallan due to cleaning taking place on the main track, the ABC has been told.

Workers from the agencies responding to the disaster could be seen inspecting a section of track where the train derailed. ( ABC News: Simon Winter )

Normally, there would be signals along the track telling drivers which way the points would be set.

But all signals between Donnybrook and Kilmore had been blacked out and the points were being operated manually by rail workers, after a fire damaged a signalling hut on February 4.

The train pilot had boarded the XPT service at Kilmore to help the driver navigate the complexities of that stretch of rail.

The tracks and signalling section involved is owned and maintained by the Australian Rail Track Corporation (ARTC).

Phillip Barker, director of Rail Safety Consulting Australia, has decades of experience investigating rail accidents and said the manual changes in place could have created increased risk.

"We've had a fire. We know the signalling system was out of use. ARTC put in a manual system of forms and authorities to move the trains through, and that is open to human error," he said.

"You increase the risk of something happening."

The president of the independent consultancy group Rail Futures Institute, John Hearsch, told AM the effect of the signalling fire would be looked at by investigators.

"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.

Deputy PM rejects union claims

Victoria's Rail, Tram and Bus Union (RTBU) said it was "deeply saddened by the tragic accident that has taken the life of two rail workers and unnecessarily injured many more".

"The Sydney to Melbourne XPT train derailment near Wallan Station last night occurred over a section of track over which was awaiting maintenance," RTBU state secretary Luba Grigorovitch said in a statement.

"Conditions were altered and V/Line drivers rightly refused to traverse this section over the past week."

The ABC understands a V/Line driver operating a train from Albury to Melbourne last Monday refused to continue along the line due to safety concerns after the fire.

But Deputy Prime Minister Michael McCormack said although investigations were still underway, "no authorities would ever let a train go on an unsafe track".

"Passenger safety is first and foremost."

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 1 minute 24 seconds 1 m 24 s Paramedics took 11 of the train's passengers to hospital for treatment.

The chief executive of V/Line, James Pinder, said the area was a "particularly complicated part of the infrastructure", where different services ran alongside each other.

He said he was not aware of the union's comments, but said: "V/Line's number one priority always is and always has been and always will be, passenger safety and the safety of our staff and that won't change in the future."

He said V/Line was operating on the track before Thursday's derailment.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 1 minute 4 seconds 1 m 4 s The train was carrying more than 150 passengers from Sydney to Melbourne.

Transport for NSW secretary Rodd Staples said the chief executive of NSW TrainLink, which operates the XPT service, had met with the family of the killed driver to offer condolences and ongoing support.

"He was a very experienced driver, he was well-known across our workforce and was much loved and all our people in TrainLink were absolutely devastated about his loss," Mr Staples said.

Long-held concerns on line

Deputy leader of the Victorian Nationals Steph Ryan said she had held significant concerns about the line "for the better part of five years".

"The reality is that this line has been beset by problems now for the best part of a decade," she said.

The North East line has been plagued by concerns for years and was described as "a disaster waiting to happen" in 2010.

The Federal and State Governments inked a $235 million deal last year to upgrade the infrastructure, but works have not yet begun.

Ms Ryan said while investigations were just beginning, "we do know this section of the line has been the cause of numerous delays on the V/Line service over the last week or so".

Five of the train's carriages were flung off the tracks. ( Supplied )

RTBU national secretary Mark Diamond said the union had serious concerns about the state of the main line track between Melbourne and Sydney for many years.

"It is important that safety authorities conduct a full and thorough investigation of the particular circumstances of this derailment," Mr Diamond said.

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".

Mr Toole, the NSW Transport Minister, said the state was working on replacing XPT trains, some of which were more than 38 years old.

"They've well and truly served their purpose over that time into regional communities," he said.

All train services to Seymour, Shepparton and Albury have been replaced by buses until further notice due to the disaster, Victoria's Department of Transport said.

'Very early days' of investigation

The ATSB will release a preliminary report within 30 days, but the final investigation could take months or even years to be finalised.

National Rail Safety Regulator chief executive Sue McCarrey told ABC Radio Melbourne that works underway on the line would be among a range of factors examined by investigators.

Key to the investigation would be the speed limit on the track at the time and the speed of the train, which would have been recorded by the train's data log.

"It's very early days to speculate on what the causes actually are," Ms McCarrey said.

Twelve passengers were taken to hospital after the derailment. ( Supplied: James Ashburner )

She said two rolling stock experts and a signalling engineer were among the team of investigators already out on site.

Ms McCarrey said she was aware of media reports that the driver told passengers over the public address system ahead of the crash that he was going to try to "make up time".

"Again, that's something else to look at as part of the investigation," she said.

"We will be interviewing a number of people to try and determine what the actual facts are what was said over the PA at the time."

However, she added that drivers could not exceed speed limits set by the safety management system which varied due to factors including the condition of the line and weather conditions.