Serious concerns over the performance of John Delaney and the finances of the FAI were highlighted to external auditors as far back as 16 years ago.
The crisis currently engulfing the association was foreshadowed in an explosive letter written by a former board member.
The correspondence sent to senior FAI officials by solicitor Brendan Dillon outlined how consultants and advisers went unpaid for several months due to insufficient cashflow.
Mr Dillon also highlighted big differences between financial projections made by then-FAI honorary treasurer Mr Delaney and subsequent accounts.
He claimed queries he raised about management accounts were met with "unhelpful and inadequate" responses from Mr Delaney, who had been elected as the association's youngest ever treasurer in July 2001.
Mr Dillon revealed the existence of the 2004 letter at the FAI's reconvened AGM last Sunday, where delegates heard a copy was also supplied to auditors Deloitte.
The firm was the FAI's auditors for 23 years, but did not seek reappointment after controversies which led to the departure of former chief executive Mr Delaney last year.
It is unclear if Deloitte acted on the information contained in Mr Dillon's 14-page letter.
Deloitte declined to answer queries submitted by the Irish Independent in relation to Mr Dillon's correspondence or say how many times it had to tender for the FAI contract during the 23-year period.
"As a statutory audit firm, we are bound by strict obligations of confidentiality in respect of audited entities," it said in a statement.
"Due to our adherence to our obligations of confidentiality, and the ongoing investigations by the ODCE and An Garda Síochána into certain matters relating to the FAI, we are unable to respond to the questions raised."
Speaking at the AGM last weekend about more recent sets of accounts, Deloitte audit partner Richard Howard said the firm was "misled" by former FAI directors.
Mr Dillon said he copied Deloitte on his letter, which was sent to then-FAI president the late Milo Corcoran and Mr Delaney in March 2004.
He had quit the FAI board and as chairman of the League of Ireland three months earlier, highlighting concerns over financial and corporate governance.
In the letter, he expressed "grave concerns" over a number of decisions made by the FAI and what he termed the "lack of information, transparency and openness in relation to the financial and operational workings of the association".
He said there were serious and onerous obligations on him under company law, and that he continued to be responsible and accountable for the activities of the association during the period he was a director. Mr Dillon requested clarification on several financial and governance issues, but says he never received a response.
He also criticised Fran Rooney, the then-chief executive who Mr Delaney would succeed in November 2004.
At the AGM last Sunday, Mr Dillon outlined some issues raised in the letter and said: "Deloitte were aware of issues.
"I wrote a very lengthy letter to the then board addressing concerns that I had at the time. A copy of that went to your firm," he told Mr Howard.
"It wouldn't have been you [Mr Howard] that was in charge at the time. I addressed issues including, among many other issues, payments to directors, projections versus reality in relation to the accounts, what was being projected and what actually was the reality, and the monitoring of expenses."
The Deloitte partner did not comment on the letter, but talking about recent accounts said the firm "went on the information provided to us".
The publication of its latest audit report, for 2018, was delayed until three weeks ago and the firm refused to confirm the FAI's status as a going concern.
Deloitte had approved all yearly accounts up to 2017, but in April 2019 it lodged a H4 complaint under the Companies Act.
The firm claimed the FAI failed to keep proper records after details only emerged last March of a €100,000 bridging loan given by Mr Delaney to the association in 2017.
The sum, repaid two months later, was concealed from most of the board and Deloitte and omitted from the annual accounts.
Consequently, when discovered, the Office of Director of Corporate Enforcement instructed the FAI to restate its 2017 accounts.
That was just one element in a review which led to a €2.75m surplus for 2017 being recorded as a deficit of €2.85m in reconstituted accounts.
A restating of the 2016 accounts also shrunk a €2.3m profit to €66,000. The belated 2018 accounts presented a loss of €8.9m.
The FAI is currently burdened by €62m of liabilities and requires a €18m bailout by January 25 to avoid defaulting on their next staff pay run.
Sports Minister Shane Ross insists liquidation or examinership are not viable options for the FAI.
In his letter, Mr Dillon itemised a number of issues, including fluctuations between revenue and expenditure projections, and bridging loans to League of Ireland clubs.
The solicitor sought a series of documents to comply with what he deemed his duties as a director during that period, but Mr Rooney claimed former directors were not entitled to that information.
Following a meeting of the full FAI council on April 3, 2004, however, Mr Rooney insisted that Mr Dillon would be offered the chance to examine the books in the presence of Mr Delaney.
Speaking yesterday, Mr Dillon said this offer was not forthcoming.