KiwiRail is disputing Waka Kotahi's claim that the Hamilton to Auckland train, Te Huia, came within 200 metres of a collision in July.
Waka Kotahi's director of land transport and general manager regulatory operations Neil Cook told RNZ this week: "The prohibition order put in place for the Te Huia service was taken in response to a situation where a commuter train carrying over 90 passengers entered the busy Auckland Metro Rail Network, coming within 200 metres of a collision with another passenger train, with the risk of multiple serious injuries or fatalities".
He said this level of risk was not present for any of the other eight trains (six Wellington passenger trains and two Auckland passenger trains) which also failed to stop for red signals this year in what are called SPAD A events. SPAD A events are defined as an incident when the train driver has failed to obey a red signal and has entered a section of track where there is the potential to encounter another rail service.
However, KiwiRail's executive general manager operations Paul Ashton said the train in question was stopped on the Onehunga train line, while Te Huia was on the southern train line.
"Te Huia was not in a section of track occupied by another train at the time of [passing the red signal], so there was no risk of immediate collision with the metro train," he said.
Of the 10 metropolitan passenger trains that have failed to stop for red signals so far this year, only the Hamilton to Auckland train, Te Huia, has faced sanction.
The risk of collision has been held up by Waka Kotahi as an important difference between the Te Huia and the other trains.
Te Huia resumed its full service into central Auckland earlier this month.