"Consequently, some of these people may have had to pay a higher amount of tax this year than they were expecting."
In the past IRD relied on people selecting their correct PIR, but the new system meant they could check whether they had.
Cavill said there could also be refunds for people who had overpaid, but those details or the average bill amount could not be provided at this stage.
"It depends on the individual customers' circumstances overall as to whether they will get a bill or a refund."
According to the IRD's website, the PIR for residents is based on their income from the last two years. The prescribed guideline rates are 10.5 per cent for those earning a taxable income between 0 and $14,000, 17.5 per cent for those between $14,001 to $48,000 and 28 per cent for those earning more than $48,001.