The June 2021 crash involved a collision between a Queensland Rail locomotive with the rear of a stationary Aurizon coal train at Westwood, about 45km west of Rockhampton.
A 49-year-old-man died at the scene and two others were injured.
Responding to the charges filed by the Office of the National Rail Safety Regulator, Queensland Rail said it would not contest the prosecution and would work to resolve the matter promptly.
"Queensland Rail remains deeply saddened by this incident and the loss of a colleague. We continue to support the family of the deceased as well as the other two drivers and their families," the operator said on Monday.
"We remain committed to operate a safe railway and to learn from this incident and do all that we can to prevent it from happening again. We want to ensure that when our people come to work, they work safe and go home safe."
The maximum penalty for breaches of this kind is $1.5 million per offence.
"(The national regulator) will allege that QR failed to comply with its safety duties as an accredited rail transport operator under Rail Safety National Law," it said on Monday.
The matter was being pursued in the interests of rail safety and to promote public confidence in rail operations, the regulator said.
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