Auckland One Rail has confirmed it requested on 24 June that the Hamilton to Auckland train Te Huia be suspended over safety issues.
On 11 July, Waka Kotahi sanctioned the train and restricted its service, after two incidents of the train failing to stop for red signals.
Auckland Transport's rail franchise manager Craig Inger said the Auckland train operator Auckland One Rail raised concerns directly with Waka Kotahi and with KiwiRail.
"Both Auckland Transport and Auckland One Rail (AOR), the company running AT's passenger rail services, wrote to KiwiRail following the Te Huia SPAD (signal passed at danger) incident to express our concerns.
"As the Safety Case holder for Auckland's passenger rail services, AOR also raised concerns directly with Waka Kotahi over the Te Huia incident."
He said AT and AOR staff were also present during KiwiRail briefings on the SPAD event, and they had a "robust conversation" about their perspectives on the incident.
Te Huia is the only service to be sanctioned by Waka Kotahi for safety, despite eight other passenger trains running red lights in the first half of this year.
Last week, Rail and Maritime Union general secretary Todd Valster said he believed Te Huia was singled out by Waka Kotahi because of complaints from the Auckland train operator and Auckland Transport.
"From there, NZTA has reacted. NZTA could possibly respond differently to the level of complaints it is getting from the regional councils."