FIFA and UEFA have both written to FAI General Manager Noel Mooney saying they're concerned over comments made this week by the Sports Minister.
Shane Ross said that Donal Conway should withdraw his nomination for re-election as the association's President.
Conway is set to be returned unopposed at next week's AGM.
Speaking about the upcoming appointment, Ross addressed Conway directly saying, "I know you have shown personal commitment these past weeks at the roadshows seeking to secure the support of the FAI members for the Governance Reform recommendations and I appreciate the recent work you have done.
"However, I must ask you to withdraw your nomination for re-election at the upcoming AGM to allow for new leadership with credible reform credentials, in the best interests of football."
Ross also claimed Mooney's appointment to the role of general manager leaves the FAI with "a very old look about it".
The European and world football governing bodies have reminded the FAI that third party interference with national associations is strictly forbidden. Sanctions could be imposed if third parties are seen to be directly influencing national associations.
The FAI say the letter will be discussed by the Board of the Association at its meeting ahead of their EGM in Dunboyne.
Minister Ross has also been forwarded the letter.
The letter itself reads:
"FIFA and UEFA are seriously concerned regarding the aforementioned 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."