KiwiRail says it left 300 passengers stranded in a stationary train in the Hutt Valley on Thursday morning for safety reasons.
The TranzMetro service from Wairarapa was stopped between the Taita and Waterloo stations for about an hour after its driver reported going through a red signal.
The train was full of people going to work. Some passengers complained of getting little information as they waited, unable to leave the train.
Other passengers say they were told the driver had to undergo interviews and drug testing.
KiwiRail will not comment on what action is being taken against the driver.
But it says as soon as the driver reported running the signal he was immediately relieved from duty under a strict safety code and a replacement driver found.
About 1000 other passengers had their travel disrupted as their trains to the city banked up behind the stationary one.
KiwiRail says it will try to speed up the process if it ever happens again.