FIFA and UEFA have written to the FAI to express concern over a letter from Minister for Transport, Tourism and Sport Shane Ross to FAI President Donal Conway asking him to withdraw his nomination to be re-elected to the role.
Both the European and World governing bodies for soccer held up the prospect of a possible suspension for the FAI and for the Republic of Ireland international teams should they be able to prove a case of 'undue influence from a third party.'
Conway has been nominated unopposed by AGM members of the FAI to continue in the role of president.
However in a letter sent to the FAI last week, Ross claimed that "the process for the upcoming election falls short of the transparency and democracy which we would expect of an organisation seeking to implement good governance practices."
The Minister referenced a meeting Conway attended with him, along with Minister of State Brendan Griffin in Leinster House on 22 May in which the FAI president reiterated a previous commitment to stand down at the AGM.
As a result Ross asked Conway to withdraw his nomination for re-election "to allow for new leadership with credible reform credentials, in the best interests of football."
However that request appears to have drawn the ire of both FIFA and UEFA who are unhappy with what they see as a possible case of third party interference into the running of the FAI.
The Secretary General of FIFA, Fatma Samoura, and the General Secretary of UEFA, Theodore Theodoridis, have written a joint-letter to Mooney.
The letter references the sections of UEFA's and FIFA's statutes which prohibits government interference in a national soccer body.
It read: "FIFA and UEFA are seriously concerned regarding the statement from the Minister for Sport.
"In this context, we draw your attention to art. 14 par. 1 let. i), 14 par. 3 and art. 19 of the FIFA Statutes as well as to art. 7bis par. 2 and art. 9 par. 1bis let. d of the UEFA Statutes, which oblige all member associations, including the FAI, to manage their affairs independently and without undue influence from any third party.
"Failure to meet these obligations may lead to sanctions as provided for in the FIFA Statutes and UEFA Statutes respectively, including a possible suspension, even if the third party influence was not the fault of the member association concerned.
"In this context, we kindly request that you communicate the foregoing to the relevant authorities and keep us closely informed on further developments regarding the matter at hand. We thank you for taking note of the above."
The letter to the FAI will be discussed by the Board of the Association at its meeting tomorrow in Meath ahead of the EGM at the Dunboyne Castle Hotel.