KiwiRail has issued an apology after a three-hour train shutdown left peak-hour Auckland commuters stranded on Friday morning.

A KiwiRail signal issue suspended all train services on the Auckland network from 7am. The shutdown forced some commuters to evacuate trains and walk along rail lines.

All passengers had been evacuated from the trains by 9am and entrances to the Britomart train station were closed off to the public.

KiwiRail was "hugely apologetic" about the disruption caused by the fault, acting chief executive Todd Moyle said.

"This was a very unusual event as not only was there a fault in our main signal operating system, but the backup also failed and we have had to revert to a third alternative," Moyle said.

All passengers who were disrupted because of the signal fault would be refunded, an Auckland Transport spokesperson added.

JASON DORDAY/ STUFF An out of service train sits in Kingsland station out of service.

Those using AT Hop cars would receive an automatic refund while those who purchased tickets would need to visit a customer service centre.

Trains started moving again at 10.32am, on a half-hourly basis, with the first one leaving Britomart.

At 3pm, Auckland Transport said trains were operating every 20 minutes on the southern, eastern and western lines. The Onehunga line was running as normal.

"Services will operate with six car units, as far as possible. Rail replacement buses will continue to operate during the afternoon peak.

"There will be automatic refunds for customers who have a registered AT HOP card and whose travel was disrupted during this morning's signals failure. Other affected customers will need to go to a customer service centre for a refund."

Earlier, Goff said he was meeting with AT to discuss what had gone wrong with the KiwiRail signals.

SUPPLIED Commuters were told to disembark at the no longer used Westfield Train Station.

"I'll also be asking how we can stop this from happening again," he said.

An Uber spokeswoman said its fares had surged due to added demand but the average price charged was less than double the amount of a normal fare.

KiwiRail chief operations officer Henare Clarke said the signal issues had been due to KiwiRail's operating system failing, along with a back-up system failing to activate.

"Some trains are now moving in the city on a third, older system while a team of 25 from around the country look to fix the issue. Investigations are centring on a controlling system in Auckland.

"The causes are unknown and being investigated."

Moyle said this was the first time KiwiRail had experienced a fault like this with the Auckland signalling control system, which had been in operation since 2011.

MANDY TE/ STUFF It is unknown when the services will be running again.

The back-up system was also in regular use.

A commuter who was taking a southern line train to work when the signal outage happened was left with no other transport options.

"The train was stopped for almost an hour and there was an announcement that something had happened which was good because it gave us all a chance to call our bosses.

"We got off the train at the Wiri station which is usually just used as a train depot but the buses around there were all so full I couldn't get on one."

She ended up having to walk to her workplace, which took an hour.

"It kind of sucks that this happened especially as they want to raise the price of ticket prices but things like this happen, I don't even know if I'm going to get a refund."

MANDY TE/ STUFF The train timetable board at Britomart has no train services showing.

Currently it costs the commuter around $10 a day to travel by train to her job and she said she was beginning to think it may be easier and cheaper to just drive.

Auckland commuter Jess Fox was stuck on a train near Newmarket for over an hour.

"No bathrooms, a few updates, the driver likened the situation to an air traffic controller who's lost his radar screen.

"I'm very late for work, I usually start at 7:30."

At 8:20am Fox said the train she was on had made it to Newmarket and passengers had been let off.

"They've terminated all other services so we have to bus from here but no rail replacements have been organised - you'd think they would have organised some over the last hour, at least there's plenty of other buses heading to Britomart."

MANDY TE/ STUFF The entrances to Britomart Train station have been closed to the public.

One Auckland commuter told RNZ she had been stuck inside a tunnel near Britomart for an hour.

"They asked us to evacuate the train and walk through the tunnel," she said.

Moyle said shortly after 8:30am trains were moving on a "restricted basis" to let passengers disembark at the nearest station.

Buses were accepting train tickets and AT HOP cards for those who needed an alternative form of travel.

KiwiRail said it was taking the issue extremely seriously.

"It's been all hands on deck since early this morning as our teams worked to fix this issue," Moyle said.

JASON DORDAY/ STUFF The Kingsland Train station was devoid of commuters after 9am.

"We'll be taking a very close look at what caused this fault and how it can be prevented from happening again."

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