Chief executive John Fullerton faced Senate Estimates late on Monday night, which is a regular appearance he makes to provide an update on rail works. But this time senators were looking for answers on the safety of the track, less than two weeks after the fatal train derailment at Wallan.

Under questions about the quality of the track, Mr Fullerton said he had heard the safety concerns raised over the past 10 years, but maintained the ARTC was still meeting its requirements under the lease agreement with the Victorian government.

He denied the track was "awaiting maintenance" at the time of the crash, but said the signal cabin was waiting to be repaired, which is why there was a pilot with the driver - both these workers died in the crash.

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"The electrics of the signal cabin were destroyed when it received a high voltage surge from a truck striking a powerline," Mr Fullerton said.

"The pilot was part of an extra safety precaution to provide the driver with some information regarding to that level crossing in particular over that 23-kilometre section."

But he said it was dangerous to connect the signal box incident with the train derailment at this stage.

"The Wallan incident is under investigation and I don't really want to speculate about causes," he said.

The $235 million in works to the North East line were still on target to be completed by mid-2021.

Senator Tony Sheldon asked about the training of the driver and pilot, and the driver's previously-raised concerns about track safety.

"When you head up any operational business, in rail or otherwise, you work hard to prevent accidents and prepare extensively in case they happen," Mr Fullerton said.

"During the accident we lost two much-loved members of the rail family.

"This accident devastated families, friends and colleagues and an industry that prides itself on safety."

The Victorian Coroner and Australian Transport Safety Bureau are investigating the derailment.

"There were two employees in our industry who went to work and never came home and we collective owe it to John Kennedy, the driver from Canberra, and Sam Meintanis, the pilot from Castlemaine, to work with investigators to understand what happened and what actions need to be taken to prevent this from ever happening again," Mr Fullerton said.

"These investigations will provide the answers we all want."

The ARTC has also pledged to co-operate with an independent audit of the railway track conducted by the Office of the National Rail Safety Regulator.

The audit will focus on the suitability of the standards the ARTC uses to maintain the track whether it meets them.

ONRSR chief executive Sue McCarrey said this would be separate to the regulator's investigation into the fatal derailment at Wallan.

"The action I've taken in relation to ARTC is about addressing the very public concerns of rail safety workers and making sure we can promote public confidence in rail safety," she said.

Border Rail Action Group chairman Bill Traill said the broader investigation into the ARTC's maintenance of the track was a big breakthrough.

He said he had concerns about signalling and did not believe the driver who died would have known the speed limit had been lowered.

"The deep-seated track issues which have persisted since the initial upgrade was allegedly completed in 2011, and again in 2016 when the ballast rehabilitation program joined the queue of failures, cannot be allowed to happen again," he said.