A HSE internal audit of the Pandemic Special Payment said there were notable control weaknesses and governance gaps that should inform future crisis response payment schemes.
It says that €712,000 of duplicate bonus payments and 63 HSE overpayments are still under investigation.
The one-off special payment was made by the government for frontline employees dealing with Covid-19 between March 2020 to June 2021.
The payment was €1,000 or €600 tax-free, depending on an employee's contracted hours.
In total, €211 million was paid to 223,000 staff.
The audit says there were payments to senior Health Service Executive managers and high appeal rates, indicating potential misinterpretation of the scheme at local levels.
A lack of early PPSN based validation for Section 38 agencies (funded but not run by the HSE) delayed duplicate payment detection.
Of the €211m paid, €88m was to HSE employees and €51m to Section 38 agencies.
Also, €72m was paid to the non-HSE and non-Section 38 workforce.
The audit, which has been published by the HSE, says there was no formal post-implementation or "lessons learned" review conducted.
