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Te Huia has been temporarily banned from the Auckland metro area, because of two incidents of running red light signals.
Waka Kotahi said the train must be fitted with a European Train Control System (ETCS) before it would be allowed back into the suburban passenger network.
But KiwiRail said it would take up to two years to design, install and test the system.
Rail and Maritime Transport Union general secretary Todd Valster told Checkpoint Te Huia had been "singled out" unfairly.
[aduio_play] "You can't go down to the road to PB Tech and just go and buy a system and put it in the train" - Rail and Maritime Transport Union general secretary Todd Valster
Other trains regularly operated on the Auckland rail network that did not have ETCS, including freight trains, shunts and the Northern Explorer passenger service that runs between Auckland and Wellington.
"The only trains that have got what they call ETCS are the Auckland suburban trains, there's no other trains in the country that have got that system."
In Wellington, ETCS versions two or three were being considered for trains on the suburban rail network, Valster said. "It's never had ETCS, but they are looking at putting that in, in the future, as an additional safety system.
"That's good, but ... you can't go down to the road to PB Tech and just go and buy a system and put it in the train, it has to have a much higher integrity to make sure that it's going to do the job that it's required to do.
"ETCS is going to come across all the fleet in Auckland at some stage, but the action of stopping Te Huia now just doesn't make sense to us."
Te Huia had run for two years "without any big issues coming up", Valster said. However, "there were some initial teething issues".
Te Huia normally carries commuters between Hamilton and Auckland, but can only run to Papakura under the current Waka Kotahi ban Photo: RNZ / Gill Bonnett
The two instances of Te Huia running red lights were still under investigation. One had happened on the Auckland suburban rail network, and the other "nowhere near" it, Valster said.
"[The drivers] typically get stood down and an investigation is taking place and then it deems whether they are responsible for that taking place or if there may be other factors that can be involved.
"That's what we should be focused on is what actually caused the incidents in the first place so mitigation or prevention can be put in place to prevent that.
"But inconveniencing the public by stopping the train at Papakura and getting them off the train and putting them on the bus or having to catch other services just seems unnecessary."
There was strong interest in more regional train services in New Zealand, he said. "Te Huia is the first modern one that's been put in place with a whole lot of other safety features that other passenger trains round New Zealand don't have."
Asked if Te Huia would survive the Auckland network ban, Valster said "fingers crossed".