Investigators will examine whether a train that derailed north of Melbourne, killing two people, was speeding to make up time on a substitute “loop” track on which automatic signals were no longer operational.

The direction of rail tracks could be a vital clue, as they were changed earlier that day for the first time in weeks, the ABC has been told.

The latest revelation comes as the train drivers’ union claimed many of its members had refused to use the part of the track where Thursday’s fatal crash happened because of a lack maintenance.

Trains had been proceeding directly through the switch for the previous fortnight, but on Thursday were redirected to a loop that skirted a cleaning detail working on the main track, according to the ABC.

Normally, there would be signals along the track telling drivers which way to go.

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

Australian Transport Safety Bureau commissioner Greg Hood said a preliminary investigation would be conducted within 30 days.

“I know everybody wants answers now but really we’re just beginning our work this morning,” he said on Friday.

The Rail, Tram and Bus Union state secretary Luba Grigorovitch said drivers had refused to “traverse” the Wallan section of track for the past week.

“The Sydney to Melbourne XPT train derailment near Wallan Station last night occurred over a section of track over, which was awaiting maintenance,” she said.

“Conditions were altered and V/Line drivers rightly refused to traverse this section.”

• Related: Transport union says track needed maintenance

The train’s male driver, 54, from the ACT and his female co-pilot, 49, from Castlemaine, were both killed on impact when the Sydney-Melbourne XPT diesel locomotive and five carriages came off tracks near Wallan Station, 45 kilometres north of Melbourne just before 8pm on Thursday.

Police said it was a “miracle” more people weren’t killed or injured among the 160 passengers on board. Many of those on board clung on for “grim death” as the engine and first carriage slid off the tracks and tipped onto their sides.

On Friday morning, the remainder of the train was still leaning off the wrecked tracks.

“I imagine, as a first responder who turned up, it would have been looking like a horrific scene,” Acting Inspector Peter Fusinato said.

“I’m very surprised there weren’t more serious injuries … quite a miracle really.”

There are reports one man was injured while trying to save the driver, while up to 20 people were unaccounted for.

A man in his 60s was taken to the Royal Melbourne Hospital in a stable condition with an upper body injury while 12 others were taken to local hospitals with minor injuries.

Five passenger cars derailed in the accident. Photo: CFA

Deputy Prime Minister Michael McCormack, who visited the crash scene on Friday, said repeatedly that federal authorities wouldn’t allow a train to travel on unsafe track.

“I reiterate – no authority would let passengers travel on unsafe track,” he said.

“We will ensure that proper answers are found for the bereaved families and making sure these sorts of things don’t happen again.

“I invite the unions to put all those matters to the proper authorities so that we can fully investigate what has taken place beforehand and of course, what took place last night.”

The federal government-owned ARTC manages and operates the track and is understood to be responsible for the signalling.

The ARTC has been contacted for comment.

After the accident, some passengers reported an onboard announcement from the driver, saying he would try to make up for lost time before the crash. It came after lengthy earlier delays caused by ongoing problems with signals on the line.

Victoria Police Inspector Peter Koger couldn’t confirm those reports on Friday morning.

It is not publicly known what speed the train was travelling at the time it came off the tracks.

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Shaken passengers were bussed to Melbourne after the crash, while others were picked up by family.

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.”

• Related: Passengers recount horror of train derailment

The man also said train staff had handed out complaint cards to passengers moments before the derailment.

The train left Central Station in Sydney at 7.40am on Thursday and was supposed to have arrived at Melbourne’s Southern Cross Station at 6.30pm.

In December, Infrastructure Australia stated the business case for an upgrade of the Melbourne-Albury North East Rail Line “should not be included on its priority list”.

-with AAP