The ministry had requested the victim impact statements of the families of Ben Rockhouse, Joshua Ufer and Joseph Dunbar be read out.
But Judge Farish said the company's admitted failure did not in any way cause the mine explosion.
Today's sentencing comes a day after former Pike River Coal chief executive Peter Whittall pleaded not guilty to 12 charges over the explosions.
The charges relate to his actions regarding safety at the mine, including methane explosion management, strata management, ventilation management, and mitigating the risk and impact of an explosion.
In a statement outside court, Whittall yesterday reiterated his deep sorrow for the losses that the Pike River families suffered.