With multiple disruptions within a span of two hours, as of 8.30am Auckland Transport said Western line services would only go between Swanson and Newmarket, not all the way to Britomart "until further notice".
That means commuters will need to transfer to another train service at Newmarket to get to Britomart.
The affects of the earlier KiwiRail track infrastructure issue had closed platforms 2 and 3 at Britomart Station, AT said.
Trains were cancelled on Auckland's Western line between Britomart and New Lynn after more track issues on the city's network.
Auckland Transport said a KiwiRail problem had been resolved by about 7am, but would still see services operate at a reduced frequency.
However, pointing to another issue, KiwiRail metros general manager Jon Knight said there was overnight damage to a set of signal points on the Western line.
The signal damage was the reason trains were unable to operate between New Lynn and Britomart, he said.
"The signal points are operating as normal and passenger trains are now able to resume operating as normal."
More disruption can also be expected for Auckland train commuters as the next stage of KiwiRail's Western line rebuild gets under way.
For seven weeks, trains between Newmarket and New Lynn will run at reduced frequencies as maintenance work closes one track at a time.
Auckland's rail operators have promised the city's trains will run more smoothly, with a new control centre providing hope of no repeat of January's commuter train chaos.