Trains on the Kapiti Coast north of Wellington restarted at 3pm on Friday after being halted for six hours by a computer software problem.
The problem caused signal faults between Pukerua Bay and Otaki and stopped metropolitan rail services from 9am.
The Capital Connection train between Palmerston North and Wellington was also disrupted.
Buses were used instead.
KiwiRail says it has fixed the computer problem, although it is not fully satisfactory and the signals could fail again.
A faulty door on the Wairarapa line also caused delays of up to 20 minutes.