IRD has uncovered a scam in which bank accounts were used to set up fraudulent direct debits.
IRD deputy commissioner Mary Craig said the department had identified who was involved and found links between them.
"We're now working with the police and the banks to investigate further and anyone who has been left out of pocket will be reimbursed," Ms Craig said.
It was not clear from IRD's statement how many customers were affected, but IRD said it had discovered only a small number of instances.
"What many people may not realise is that we have the ability to track all movements throughout people's secure myIR accounts and there are alerts built in to let us know when anyone is attempting to do anything untoward."
The scam was not related to IRD's automatic tax assessment process which was underway, she said.
Anyone who noted suspicious direct debit payments from their bank account was urged to contact police.
