"A Senior Payroll Officer at DCIS checked the message within the Transaction Message Report however the payment was processed with the employee subsequently being paid A$492,176.00, instead of A$4921.76.
"DCIS further advised that due to the quantum of the overpayment, the payee, who worked remotely with no relief colleague, needed to physically attend their bank in an urban centre to authorise the return of funds to the NT Government thus there was a delay in the return of the overpayment.
"The overpayment was returned in full on October 16, 2017, when the payee was able to present at the closest branch of the bank."
The DCIS told the Auditor-General an "internal business review was undertaken following the large salary error noted".
"Actions were identified to strengthen processes and reduce the risk of overpayments through human error, which are mostly implemented," it said.
Those included a "re-examination of high-value salary payments", system and process enhancements and "refresher training for payroll staff with audit control responsibilities".
"DCIS processes over 1.2 million payroll transactions annually for the NT Public Service, with system requirements necessitating manual processing for a substantial number of transactions," it said.
"The salary overpayment total represents around 0.2 per cent of the NTG's annual payroll, with overpayments primarily caused by timing delays and human error."
As the employee agreed to immediately return the money, the issue was not logged in the NT Government's Payroll Overpayments Database. Overpayments recouped within a fortnight are classed as "salary adjustments" and also not captured in the data.
The Auditor-General's report found there were 743 overpayments in the period from July 1, 2017 to January 31, 2018, with 404 payments (A$646,839) fully recovered and 242 payments (A$262,450) partially recovered, leaving 97 payments (A$767,287) outstanding.
The largest overpayment of A$25,273, recorded as being due to "having personal leave with pay processed in error whilst on leave without pay", was still outstanding.
Last October, a Sydney lawyer got a similar shock, finding herself A$24.5 million richer after NAB mistakenly paid out her mortgage and gave her A$24,544,780.16 to redraw. Clare Wainwright told AAP she knew she "couldn't get away with playing the dumb card" and spend the money.
In 2016, a Malaysian student who went on an 11-month, A$4.6m spending spree after Westpac mistakenly gave her an unlimited overdraft was charged with dishonestly obtaining financial advantage by deception and knowingly dealing with the proceeds of crime.
But prosecutors dropped all charges against 21-year-old chemical engineering student Christine Jiaxin Lee in December last year after a similar case involving a man charged with fraud for withdrawing A$2.1m from ATMs was thrown out of court.