Athlone Town Football Club has called for a submission to FIFA and UEFA that was written by FAI Council member Nixon Morton to be formally withdrawn.
The submission outlined concerns around governance issues in the Memorandum of Understanding signed by the government and the FAI that enabled funding to be restored to the football body.
Athlone Town say they do not share any of the concerns expressed by Morton, nor do they believe that those concerns are shared by the vast majority of those involved in Irish football.
Morton believes, as a member of the senior council of the FAI, that he is charged under rule to be responsible for monitoring the activities of the FAI and, in particular, the board's governance of the Association.
His submission was prepared last Thursday.
On Friday, a copy was sent to FAI president Gerry McAnaney and on Monday a copy was emailed to all 79 senior council members of the FAI.
In a lengthy statement, Athlone air their strong disagreement with elements of the submission.
They also say that "acting CEO Gary Owens and acting Deputy CEO Niall Quinn have inherited a mess".
The statement reads: "The board of Athlone Town AFC would like to state publicly that it does not share any of the concerns recently expressed by FAI Council member Nixon Morton to other Council members, as well as UEFA and FIFA.
"The contents of said letter, received in recent days by ATAFC chairman Mr John Hayden along with other FAI Council members, made references to and raised concerns about the FAI's interim board and governance at the association.
"Having considered the letter's contents the board of ATAFC would like to make it crystal clear that it in no way supports, shares nor endorses any of the concerns expressed by Mr Morton.
"Nor does ATAFC believe that these concerns are shared by the vast majority of those involved in Irish football.
"We also believe that the timing of Mr Morton's intervention, given the extreme circumstances that prevail globally due to the Covid-19 pandemic which has all levels of the game in a forced hiatus, is regrettable.
"After a period of much turmoil within Irish football, everyone involved in the game needs to work together and get football back on its feet. This letter adds nothing to the tough task of repairing the FAI's public standing.
"Having considered the communication in full ATAFC is calling on Mr Morton to formally withdraw his letter with immediate effect.
"Mr Morton raises several issues about the FAI's interim board and governance at the FAI.
"ATAFC believes acting CEO Gary Owens and acting Deputy CEO Niall Quinn have inherited a mess, most certainly not of their making.
"It is not ATAFC's role to praise, nor criticise either individual over what they have done since they assumed their respective roles at the FAI.
"However the club's position is that the interim board should be allowed get on with their jobs, which have been hugely complicated by the pandemic.
"In his letter Mr Morton cites concerns about governance and how the independent chairperson and other senior executives at the FAI were appointed.
"We note his suggestion that the process may have been subject to 'inappropriate influence' and that the highest standards of governance were not applied.
"These are very serious allegations, but we note that no evidence at all is supplied by him in his correspondence to back up his claims.
"If there is any person attempting to exert inappropriate influences over the FAI's affairs then Mr Morton should be able to identify those persons, and set exactly when he believes their goals to be."