ACC will refund over 300,000 business customers after historical overpayment issues were discovered.
The overpayments go back to 2002 and total around $100 million, or 0.37 percent of the levies collected from the Earners and Work accounts over that period.
"We will begin refunding customers this month," said Phil Riley, head of ACC's business customer service delivery. But he said it may take until April next year to complete the process.
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Mr Riley emphasised ACC will be paying interest on the amounts.
He said ACC will refund all first-year levies collected since 2002 from self-employed customers, who worked fulltime averaging over 30 hours per week for the year.
That comes to around 106,000 customers and equates to approximately $36 million in levies.
The remaining $64 million will be refunded to around 200,000 businesses that paid provisional invoices over the same period, in "situations they were not required to do so."
"We very much regret the overpayments, and apologise to anyone who made a payment that was not required," said Mr Riley.
He said the average refund works out at around $340 (excluding GST) for first-year self-employed, and $415 (excluding GST) for provisional payments.
"ACC has been true to the intent of the regulations that newly self-employed people - like all business owners - should pay a levy," said Mr Riley.
"However, we discovered last year that since 2002, the regulations have been drafted in a way that does not provide for the levying of first-year self-employed to occur."
He said the organisation became aware of the blunder while preparing to replace the old levy system, which "included a legal check that the new system would be compliant with regulations."
"When we found the problem, we immediately stopped invoicing all newly self-employed people."
Preparations to migrate data to ACC's new levy system uncovered a second issue of provisional invoices being paid by businesses that had ceased trading or changed their business structure but not informed ACC.
The new levy system will provide a "permanent fix" to these issues and allow "automated reimbursements" to customers in the future, Mr Riley said.
ACC has drawn scrutiny the past few months after it proposed higher levies for motorists in New Zealand, which could see petrol prices increase by almost 2 cents a litre.