The XTP train service from Sydney derailed in Wallan, north of Melbourne, in February 2020 after travelling at more than eight times the speed limit through a re-routed section of track.
Experienced train driver John Kennedy, 54, and train pilot Sam Meintanis, 49, died and eight people were seriously injured in the crash.
NSW Trains, which operated the service, faced Melbourne Magistrates Court on Monday after the Office of the National Rail Safety Regulator brought two criminal charges against it.
The charges include contravening Rail Safety National Law in Victoria by failing to carry out safe systems in its railway operations, which exposed individuals to risk of death or injury.
NSW Trains is accused of failing to develop and implement risk control measures, which eventuated in the death of Mr Kennedy and Mr Meintanis and serious injuries to passengers.
This included a failure to provide up-to-date safety information to drivers before each journey, court documents stated.
NSW Trains is also accused of failing to adequately instruct, inform, train or supervise its rail safety workers to reduce or eliminate the risk of a trail derailment.
The court on Monday heard prosecutors were deciding whether the charges will be dealt with as summary offences, or will be tried in a higher court as indictable offences.
The 2020 crash prompted a series of safety actions by the Australian Rail Track Corporation and NSW Trains.
An interim report released by the Australian Transportation Safety Bureau last year found the train entered a rail loop at Wallan travelling at almost 130km/h, despite a 15km/h speed limit in place through a re-routed section of track.
NSW Trains has since changed procedures to include confirmation by train crews prior to starting their day that they have received critical safety information.
The matter will return to court on November 30.
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