Federal government agencies will likely face a bill for hundreds of millions of dollars in unpaid superannuation, with the AFP alone having to fork out $59 million to underpaid employees.
It comes as the tax office recently began a process to repay staff whose superannuation had been incorrectly calculated due to the omission of a rent allowance for deployed staff.
Former staff at the Foreign Affairs Department, AFP and Home Affairs Department say they were underpaid superannuation for years due to the miscalculation of allowances.
The affected staff claim that across government it would amount to hundreds of millions of dollars and thousands of staff out of pocket.
Former public servants who were underpaid have also raised concerns the government superannuation system lacks oversight, as it remains the responsibility of individual agencies.
They also fear the matter will not be resolved before the legislative instruments available to secure the unpaid money expire. For instance, the Fair Work Act has a statute of limitations of six years to secure claims.
An AFP spokeswoman advised that due to a change to wording in a collective agreement, some allowances became eligible in superannuation calculations but had been omitted unconsciously.
The AFP identified more than 9000 employees who were eligible for one of the allowances and the latest estimation of superannuation owed was $59 million, the spokeswoman said.
The $59 million is expected to grow as the 2019-20 financial statements will take into account another year of accumulation.
"Due to the complex nature of the adjustments required, the correction process will take some time as we work through each members individual situation," the spokeswoman said.
"The AFP is committed to delivering the best possible remuneration and working conditions for AFP staff."
The figures relate to numerous allowances specific to the AFP and not the rental allowance, which the other departments are alleged to have omitted from superannuation payments.
The Home Affairs Department said it was still reviewing claims on a case-by-case basis and would not comment on cases under review.
A DFAT spokesperson said the department was reviewing the claims relating to unpaid superannuation and consulting with the Finance Department and other agencies.
The Finance Department, the owner of the bureaucracy's superannuation laws, has steered a working group to advise departments on their obligations.
It is understood that on advice from the working group the tax office has begun calculating what is owed to affected employees and paying back superannuation where necessary.
It coincides with the end of the moratorium on unpaid superannuation offered by the tax office to businesses which ended on September 7. The scheme allowed businesses to declare unpaid superannuation and avoid paying penalties.
A tax office spokeswoman confirmed the agency was consulting with the working group but said it was still determining if the rent-free allowance should be included in superannuation calculations.
"If the value of rent-free accommodation should be included in the superable salary, the ATO will advise the Commonwealth Superannuation Corporation of the amended superable salary," the spokeswoman said.
She said the ATO had been contacted by two former staff in relation to the matter and was investigating whether other staff were impacted.
The Finance Department would not confirm what advice it had given to the tax office or other departments.
A spokeswoman advised the working group was facilitating information sharing across government on the issue and advising on legislative requirements.