The Northern Territory Government will fork out more than $30 million after discovering it had been underpaying superannuation to 56,000 current and former public servants over a decade.
The underpayments were due to the Department of Corporate and Information Services misinterpreting laws in several areas, including recreation leave loading, termination or redundancy notice periods and parental leave.
At the same time, some staff were overpaid including 14 current Territory MPs who were overpaid about $36 000, equating to more than $2,571 each.
"We apologise to our current and former staff who may be affected by either these under-or over payments," the Commissioner for Public Employment Vicki Telfer said on Thursday.
"We are focused on paying our employees their entitlements, and will pay the correct amount of superannuation, plus interest, for all affected current and former employees."
Ms Telfer said the situation came to light following advice published by the Australian Taxation Office relating to rules for the application of superannuation to recreation leave loading.
The DCIS identified it has been underpaying and overpaying some superannuation entitlements for staff for periods of up to 10 years.
The clarification had affected a number of employers across the country, she said.
The combined value of the underpayments is estimated at more than $30 million, which includes $20 million in underpayments and a further $10 million in interest plus administration fees payable to the ATO.
About 16,000 current and 41,000 former affected employees are owed about $350 each (excluding interest and fees).
They would be personally notified and the unpaid amounts, plus interest, will be paid into affected staff's superannuation accounts, DCIS chief executive officer Kathleen Robinson said.
Some higher paid employees were also overpaid, with about $6.5 million going to 390 current and former employees..
That would be recovered, although many of the overpayments were for relatively small amounts and the first $2000 would be waived and not have to be paid back, Ms Robinson said.
The payroll system issues had been addressed to ensure superannuation was now paid correctly and on time, she said.