Unite Union has accused McDonald's of stealing more than $9 million in employee wages.
The union says the fast food chain deliberately denies many employees their legal entitlement to an alternative holiday or lieu day for working a public holiday.
It has also accused McDonald's of denying workers pay for a public holiday when they were entitled to it.
"From wage and time records we have received and analysed, it seems clear that on average each McDonald's worker has missed out on this entitlement at least twice a year," Unite national director Mike Treen says.
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McDonald's recognises it "may have an issue" with annual leave calculations, but insists it's "committed to do everything we can to pay whatever is owed to current and former employees".
"As with many companies, when questions were raised about how certain aspects of the Holidays Act 2003 were interpreted, we reviewed the processes and calculations used through our company-owned and franchised restaurants," a spokesperson says.
McDonald's claims it has conducted reviews of its interpretation of the Holidays Act with audits from "third-party payroll experts".
"We believe this is in accordance with the Holidays Act," a McDonald's spokesperson says.
Unite Union first wrote to McDonald's three years ago about the need to fix how annual leave and other Holiday Act entitlements were being calculated, Mr Treen says.
"At first, this centred on a failure to calculate annual leave correctly. After some delay, the company said they would fix everything that was owed, and go back six years from when we first wrote to them - a total of nine years now.
"With 9000 crew losing on average two days' pay each year, the lost wages could be worth over $1 million a year - a total of over $9 million for this mistake if taken back nine years."
Mr Treen says Unite Union is working with the Ministry of Business, Innovation and Enterprise (MBIE) to remedy the alleged problem.
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He references a case from 2017, which saw fellow fast food joint Wendy's criticised for incorrect calculations of day-in-lieu entitlements, or pay for a public holiday.
"What McDonald's and Wendy's had done was insist that a worker had to work the same day as the public holiday three weeks in a row before the holiday.
"We asked McDonald's to voluntarily accept this judgement and incorporate the adjustment needed into their planned remediation for annual leave that was underpaid in the past. They refused."
But McDonald's says its case was different to Wendy's in regard to public holiday entitlements, because it agreed a method of calculating alternative holidays and lieu days with Unite Union.
The union says it has asked McDonald's for wage and time records so it can calculate how much its employees are owed.
"That $9 million needs to be added to people's pay before the company recalculates a correct payment for the annual leave they owe," Mr Treen says.
"McDonald's have refused to confirm they will do that so we have written to MBIE to make sure it is included in their audit of what McDonald's owes.
"It's not good enough for wage theft to be simply compensated for at the value of what was lost. There is no incentive for the company to make sure it never happens in the first place."