Honorary treasurer of the FAI John Delaney has been asked to take the position of chief executive on an interim basis.
At a meeting in CityWest, the Board and the National Council of the FAI unanimously requested that Delaney become the temporary successor to Fran Rooney.
Delaney requested time to consult with his employers and his family, which has been granted.
After the announcement, FAI president Milo Corcoran said that it was not in the association's plans to advertise the post before January 1 as requested by the Government on the recommendation of the Genesis Report and gave no indication of the length of Delaney's appointment, should he choose to accept it.
However, Minister for Sport John O'Donoghue has opposed this decision and said that he saw no basis for further engagement by the government with the FAI if they did not comply with the request to advertise the post.
Speaking on RTÉ's 6.01 News the Minister said: "I've no wish to have any confrontation with the FAI. All we're trying to do is ensure that in the future the FAI is run professionally."
Although Milo Corcoran later said that the timeframe for any appointment would be discussed with the government, the Minister said: "We have already stated what the timescale is".