AT said customers could use bus routes 30 or 309 and scheduled buses are accepting rail tickets.
AT said a track infrastructure issue at Britomart is to blame for the rush-hour disruption.
KiwiRail general manager Metros Jon Knight said about 6.50am they lost signals detection at a set of points, which allow trains to switch between tracks, in the approach to Britomart Station.
“Because of where the points are, no trains are currently able to enter Britomart. Southern and Western Line services are ending at Newmarket and Eastern Line services at The Strand.
“Our signals staff are on site. They are currently working on the issue and will aim to fix it as quickly as they can.”