Reports that the former chief executive of the FAI provided a loan to the organisation "have raised serious questions", Ireland's sports minister has said.
Shane Ross said Sport Ireland was "engaging" with the FAI over claims it received a loan of 100,000 euro from its former chief John Delaney.
Sport Ireland is expected to provide the minister with a report into the matter.
"The recent media reports regarding a loan provided to the FAI by its CEO have raised serious questions about governance and financial control at the FAI," Mr Ross said.
"In the interests of due process and in the interest of national justice it is important that Sport Ireland's engagement with the FAI will be given the necessary time to ensure all matters are considered thoroughly.
"Therefore I do not want to make comment on any possible outcome from this ongoing process."
Mr Ross was addressing questions from Fine Gael's Noel Rock, who called for an independent examination into the FAI's management and finances.
Speaking in the Dail, he said: "That means investigating everything – from top to bottom – associated companies, boardroom expenses, everything," he said.
"On corporate governance in the FAI, it's clear that it is shambolic.
"We have all been taken aback by the ongoing corporate governance and financial issues within the FAI."
Referring to a report on senior management structures which led to Mr Delaney's new role in the organisation, Mr Rock said that it was "incredible" it has been produced in its entirety in just six weeks.
"No redrafting required and the contents of it was acted upon by an unanimous vote of the board leading to the announcement of a brand new position for John Delaney," he added.
"This absolutely stinks.
"Does the minister believe that taxpayers' money is being deployed effectively, does the minister not believe that now is the time for an independent examination into FAI's corporate governance?
"It's time we look at where taxpayers' money is going as it's clear there are omissions in the information being supplied.
"On finance, I have spoken to current and former employees of the FAI and I am disturbed by what I am hearing.
"If the FAI won't clean up its own house, then we should at least work to protect the taxpayer."
Mr Ross told the Dail that Sport Ireland provided the organisation with 2.9 million euro in funding in 2018 and 2.7 million euro in 2017.
He said that Sport Ireland has "robust arrangements" in place to monitor the funding it provides to sporting bodies.
He said that the FAI is required to submit copies of its financial statements, which must include a statement from its auditor.
The FAI is audited by Sport Ireland every three years. The next audit is to take place later this year.
Mr Ross added: "I am satisfied that the existing controls in place are robust. As we have seen in the past, failures in governance within sporting bodies unfortunately damages reputation."
