The prohibition notice from Waka Kotahi to Kiwirail follows two incidents involving the train.
The Te Huia train has been temporarily banned from operating in Auckland following two incidents.
In a statement, Waka Kotahi said it had issued the prohibition notice to KiwiRail, preventing Te Huia passenger rail service from entering the Auckland metro area because of recent Signal Passed at Danger (SPAD) incidents.
The notice meant Te Huia's route, which usually ended at The Strand in Parnell, would terminate at Papakura from this afternoon.
Buses would replace the trains within the Auckland metro area.
Waka Kotahi said two SPAD incidents had been reported by KiwiRail involving Te Huia this year as it travelled between Hamilton and Auckland.
"A SPAD A event is 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 for conflict with another rail service.