Kiwirail has not discussed the circumstances of the incident because of the investigation.
Less than two weeks later, another freight train collided with a wood chipper being used by Downer in Carterton.
It was reported that contractors were working on one side of the tracks and were moving the chipper to the other side when it became stuck.
They tried frantically to free it before it was wiped out by a log train travelling south.
Nobody was injured.
Another charge alleged that on August 11, Kiwirail failed to take action to protect Tree Scape Limited contractors, which "was likely to cause serious harm".
A train between Masterton and Featherston had to make an emergency stop to avoid hitting a digger and its driver, who were on the tracks working on the rail bridge over the Tauherenikau River
The overnight freight train was travelling north and stopped about 150 metres from where the digger was, Kiwirail said at the time.
Two of the charges before the court carry a maximum penalty of $250,000, while the others could result in a $500,000 fine.
