Sport Ireland says the FAI has not sufficiently explained a €100,000 loan given to the organisation by former CEO John Delaney.
The governance body, which part funds the FAI, says it was never made aware of the loan until media reports in the last few weeks.
It recently emerged John Delaney loaned the FAI the money to address what it described as cash flow problems or a 'bridging' loan.
Sport Ireland says it was never made aware of the loan despite it being in the terms and conditions of grant approval that any deterioration in financial situation is flagged.
The head of Sport Ireland is due at an Oireachtas Committee tomorrow - and these claims are from John Treacy's opening statement.
He says they have sought an explanation from football's governing body.
However Mr Treacy says the reply "did not sufficiently explain the circumstances of this loan and its repayment, nor fully address the matter of compliance with Sport Ireland’s Terms and Conditions of Grant Approval."
Sport Ireland gives the FAI more than €3M a year in funding.
The statements notes that three separate audit firms in the past have assured the organisation that the money is accounted for and being used properly.
Sport Ireland has no role in funding the professional side of the FAI - which would include the Salary of the CEO and rental payments that were made to John Delaney.
