Auckland Transport issued a number of alerts afterwards, warning commuters to expect delays and cancellations on the Southern Line.
Services were being stopped at the Homai station and passengers were being told to catch route 33 buses between Papakura and Homai.
Delays were still evident at 9.30am, when scores of people waited to be transferred to buses and train services at Homai.
A Herald reporter said many people were waiting at the Homai station just after 9am.
"Commute a nightmare this morning,'' she said.
Train services in the west of the city were also affected because of a signal fault around 6.30am.
Western Line services were being stopped at Henderson as a result, but resumed around 7.30am. Passengers were being warned to expect delays.
Meanwhile, those catching rail services in Wellington also dealt with delays due to frost on the overhead power line.