Auckland Transport (AT) is asking HOP card holders to reset their automatic top-ups and to pay outstanding balances on their cards.
Only customers who use the auto top-up function and keep getting 'insufficient funds' alerts when tagging on need to take action.
It comes nearly two weeks after a cyber attack crippled parts of AT's HOP card system, including EFTPOS and credit card payments.
Stacey van der Putten from AT's public transport services thanked the public for their patience and apologised for the inconvenience.
"We've worked really hard to bring all of the systems back online, but there have been a few residual issues which we are still resolving," she said in a statement on Tuesday.
While AT rebuilt the system last week it couldn't charge customers' debit or credit cards - so all auto top-ups were disabled between Wednesday September 13 and Thursday September 21.
No customers were charged during this time.
"We haven't charged customers for trips they have not taken, but customers may find they have a negative balance for trips they have taken in the past week that have not been covered by an auto top-up," van der Putten said.
She said it was an unforeseen issue.
"Essentially, because the system was unable to charge customers for their auto top-up within seven days, the system has reversed the attempted transaction and disabled their auto top-up."
Affected customers can continue to use trains, buses and ferries as normal until the end of Wednesday - even if they get error beeps as they tag on.
People who don't use auto top-ups should find their cards working normally.
Meanwhile, Reddit users have shared their recent gripes with their HOP cards.
"I somehow now owe $54 on my HOP card, when I was $20 in credit on Saturday," one person wrote.
"Auto top-up triggered when my balance went below $10 on Thursday, but instead of adding $20, it added -$20 putting me into negatives and preventing me from tagging on anywhere," said another.
A third user who appeared to be from AT had more of a clue.
"This is not a charge to your card. This is our system undoing top-ups you did during the outage as they were never actually charged on your payment method."
A fourth chimed in with the solution in the meantime.
"They have extended the grace period because of the hack. Try tag on when you get the error sound the driver will wave you on."
What to do if you've been affected:
- Top-up your AT HOP card to cover any negative balance
- This can be done by visiting a customer service centre, a top-up machine, or a HOP retailer (online top-ups are also now available, but take longer to process)
- Re-enable your auto top-up online
- Tag on any bus, train or ferry to process payments to your account
