Despite being aware other passenger trains were running red lights, Waka Kotahi only sanctioned the Auckland to Hamilton service, Te Huia.
At the time Te Huia was sanctioned over safety concerns on 11 July, Waka Kotahi knew of eight other passenger trains which ran red lights earlier in the year.
But Te Huia alone faced sanctions.
Waka Kotahi said it was concerned the train was a safety risk after two reports of it running through a red signal.
The train was forced to stop its service on the outskirts of Auckland in Papakura. However, two weeks later on 28 July the full service was told it could return from 7 August.
Information provided by Waka Kotahi to RNZ under the Official Information Act showed between 1 January and the beginning of July, 27 other red signal events were reported across the network. Two of these were Te Huia, two were other Auckland metro trains and six were Wellington metro trains.
The other 17 incidents involved freight trains and maintenance vehicles in locations such as Tauranga, Mt Eden, Huntly and Dunedin.
During a Transport and Infrastructure Select Committee briefing this month, Waka Kotahi land transport director Neil Cook confirmed Te Huia was not the only train to report a safety issue on the Auckland network, even though it was the only service to receive a sanction.
He told the committee that "situations may be similar, they are never the same".
For this reason Cook said a broad-brush response was not possible.
"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. This level of risk was not present for any of the [other safety] events in the Wellington Metro area to date in 2023."
RNZ has asked for more information on passenger numbers and train distances for the Wellington trains.
Transport Minister David Parker said he had confidence in Waka Kotahi as the train regulator and that questions on whether other trains should face sanction were for the transport agency to answer.
"I take safety issues very seriously but we have a safety regulator for rail and it's Waka Kotahi, not me."
Waikato Regional Council said it was surprised Te Huia was singled out by Waka Kotahi when eight other passenger trains had run red signals this year. Councillor Angela Strange said Te Huia might have been unfairly targeted.
"We were given the reason that it was a passenger train, and that's why it was [sanctioned]. Knowing now that there were other passenger trains which were treated differently - yeah, we've got a few questions."
Strange said the sanction affected Te Huia passengers, but since returning to its full route customer satisfaction and numbers were at an all-time high.
"The resurgence in numbers and feedback we've received shows how valued Te Huia is, and this is reflected in the excellent customer satisfaction survey results."
At the time Te Huia faced sanction, questions about whether it was justified were raised by groups such as the Rail and Maritime Transport Union.