AT said multiple temporary speed restrictions are in place around the city, enforced by KiwiRail which owns, controls and maintains the tracks.
Tracks were replaced in several places over Queen's Birthday weekend but there is further work to be completed on the Southern line.
"Most of these locations have been identified as needing the train tracks to be completely replaced," AT said.
"KiwiRail has assured us that the track is safe. These speed restrictions help maintain the track condition until maintenance work can be completed."
Auckland Transport said it is working with KiwiRail and Transdev to resolve the issue as soon as possible with planned maintenance.
"We find these delays and cancellations incredibly frustrating, as many of our customers will do, and we apologise for this," the organisation said.
On Tuesday last week, commuters were told to take alternative public transport after an overhead line fault led to cancellations.
The fault affected the Southern and Eastern lines but also hit the Western line as trains and crews were being repositioned, AT said.
