The Comptroller and Auditor General has said that the Sea Fisheries Protection Authority overpaid staff to the tune of €861,000 over three years.
Seamus McCarthy told the Public Accounts Committee that the overpayments have now been written off.
While the money was written off last year, it was paid over "perhaps three years".
It was the result of a "misinterpretation at a whole of agency level".
Mr McCarthy said it "goes back a number of years" and relates to advice the organisation got from Department of Public Expenditure and Reform.
The department said that "certain allowances weren't to be included in the FEMPI (Financial Emergency Measures in Public Interests) cuts".
It then emerged that the allowances should have been included in the cuts.
However, "staff had continued to receive salaries at the higher level".
The matter has been "to and from between the organisation and DPER over a number of years", he added.
A proposal to recover the money from staff was abandoned after an industrial relations process, and it was written off.
Fianna Fáil Deputy Paul McAuliffe said the "substantial" overpayments seemed to be a "disproportionate percentage of their payroll" compared to other organisations.