As many as 2000 Immigration and Border Protection Department employees have been threatened with debt collection procedures after being overpaid in leave entitlements.
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Labor slammed Immigration Minister Peter Dutton over the mistake on Friday, days after staff across agencies within the department were told a computer error had seen overpayments in leave calculations.
Staff have been told to agree to plans to repay the money within two weeks through either deductions from their annual leave entitlements, from future leave or from their pay packets.
A significant audit of leave entitlements has been completed as a result of the "systems error".
Staff have been told leave balances are now correct.
Overpayments of $100 or less are required to be repaid within a fortnight, with a sliding scale in place for larger amounts.
Debts up to $300 can be repaid within two fortnightly repayments while debts of up to $1000 must be repaid over three fortnights.
Staff who received between $1000 and $3000 in overpayment must return the cash within six fortnightly cycles and debts up to $5000 must be repaid within eight fortnightly repayments.
Debts above $5000 are subject to decisions by Finance Department delegates.
Officials apologised for the error but warned staff it reserves its right to recover the cash through available legal avenues. Anyone who doesn't agree to a repayment plan faces debt recovery management processes.
The Community and Public Sector Union is advising staff to dispute the debt amounts, which the department said was between one and five days in most cases.
Opposition immigration spokesman Shayne Neumann and employment spokesman Brendan O'Connor placed blame with Mr Dutton, who they said was responsible for poor management over two years.
They accused him of being a "tick and flick" minister.
"Peter Dutton's incompetence as Immigration Minister has been exposed yet again with the people who protect Australia's borders and the integrity of our visa system being handed the bill and forced into inflexible repayment schemes due to his failure to manage his department.
"How was this situation allowed to go unnoticed for two years and why is Peter Dutton threatening to release debt collectors on staff in his own department?"
"Peter Dutton is a tick-and-flick minister and this 'systems error' adds to the ever-growing list of times he's failed to appropriately manage his department."
A spokeswoman said the department did not use debt collectors. Mr Dutton has been contacted for a response.
On Thursday, Prime Minister Malcolm Turnbull confirmed Immigration boss Michael Pezzullo would lead the new department.
