KiwiRail chief executive Jim Quinn said KiwiRail was working closely with Veolia in order to get trains moving again.
Mr Quinn said an urgent investigation is underway to understand the cause of the outage. "We are taking the situation very seriously," he said.
The outage only affected the Auckland metropolitan network and train services elsewhere in the country were operating as scheduled.
Trains in between stations were forced to pull up into platforms, allowing passengers to disembark, after the outage.
Veolia Transport said it was trying to source as many rail bus services and taxis for customers on the network as it can.
The fault at KiwiRail's National Train Control in Wellington, which controls Auckland signals and radio control, occurred about 4pm.
Limited services on the Eastern line started running just after 5pm, with all signals back up and running by 5.30pm.
But Britomart was packed with frustrated commuters at about 4:30pm.
A Britomart worker said rush hour traffic meant it would take "a long time" to replace trains with rail buses.
Rail tickets are accepted on the following Buses: NZ Bus, Metro link, Waka Pacific, Howick & Eastern and Go West.
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