Sports Minister Shane Ross called it shocking and said the FAI isn't fit to handle public funds.
FAI Independent chair Roy Barrett has welcomed a financial agreement that he says "safeguards" the future of the association.
Sport Ireland will restore funding to the FAI to the tune of 2-point-9 million euro annually, doubling that figure for years 2020 to 2023.
An interest-free loan of 2-point-5 million euro will be provided each year from 2020 to 2022 to safeguard their interest in the Aviva Stadium.
Minister for Sport Shane Ross says there will be no programmes of compulsory redundancies at the FAI.
The laying bare of their accounts comes just weeks after a sponsor of 10 years, Three Mobile, pulled their support.