Galway United and Shamrock Rovers will play Premier Division football next season but Waterford United have been demoted to the First Division while Dundalk, who won an end-of-season play-off against Waterford, failed to get into the top flight.
The FAI last evening revealed its hand following months of consultation with their Independent Assessment Group (IAG), charged with assessing on and off-field criteria to rank clubs ahead of next season's FAI-run league.
Clubs were ranked on the basis of points scored from their on-field achievements and finishing positions over the past five seasons. Crucially, though, clubs were also graded on off-field criteria, including attendance, infrastructure, governance, strategic planning, finance, youth development and marketing.
But while results of the club's on-field scoring were made freely available, off-field points were not released into the public domain, with the FAI and IAG stressing "confidentiality" among clubs.
"I think confidentiality must be respected at this juncture," FAI chief executive John Delaney said. "Clubs need to fully understand the reasons first."
Des Casey, who chaired the assessment group, said the process was conducted in a "fair, equitable and transparent" basis but he stood by the group's decision not to reveal details of their off-field findings.
"That's just the way the points worked out," he said. "There is nothing you can do about the scoring criteria, it's a fact of life. Significantly for Dundalk it was not good enough to get them across the line."
Both Waterford and Dundalk supporters have hit out at what they see as a lack of transparency in the process and, indeed, are demanding a clearer breakdown of the scoring process for their respective teams.
A number of clubs, however, subsequently revealed their off-field scores to the media and, as it transpires, Galway finished with a combined total of 649 points (out of a possible 1000, 500 for on-field and another 500 for off-field), with Waterford totalling 632 and Dundalk 595.
Dundalk manager John Gill said the decision not to promote his team - who finished one spot ahead of Galway in this season's first division - was "stomach churning".
"I feel the club's players have been let down and the supporters have been let down," he said. "I thought fair play was still part of the game but obviously it's not.
"We had a player in the second leg of the play-off taken away in an ambulance, put in hospital having nearly swallowed his tongue. If the play-off was indeed a meaningless two games why did they put player's safety at risk and make them play?"
Waterford director Paul Cooke was visibly stunned and irate by the IAG's decision to demote his club. "We are astounded, absolutely astounded," Cooke said.
"It would appear the average from what we've seen is about 348 points for off-the-field (scoring), we scored 295. We're astounded that somebody else scored 20 per cent more."
The Waterford board of directors will now meet during the week to discuss their situation.
There is, however, no appeal process available to both Waterford and Dundalk, with Delaney stressing that clubs "knew what they were signing up to" when they voted earlier this year for reform.
But both clubs could yet go down a legal route although neither Waterford nor Dundalk have indicated a willingness to do so yet.
Delaney - himself a Waterford man - is now confident everything is being done to bring the league "where we want it to be" but he said in doing so there was always going to be "tough decisions to make."
"The supporters and everyone else understands that the clubs bought in and agreed to this process," he said. "Everybody knew what the rules of engagement were, they were made very clear."
Delaney also expressed "a certain amount of sympathy" with both Waterford and Dundalk for having to play a meaningless end-of-season play-off but was quick to deflect criticism away from the association saying it was an eircom League decision to stage the games.
Casey - a Dundalk man - agreed and said the two games were "entirely counter productive" and "grossly unfair to the players and managers involved."
The IAG will provide a debriefing facility for any club that requests a detailed breakdown of their scores. Clubs will then have until January 17th to sign participation agreements to play in both the Premier and First Divisions.
This IAG committee was composed of former FAI honorary secretary Des Casey, former Dublin city manager John Fitzgerald, current Charlton Athletic director Richard Collins and former Irish Sports Council chairman Pat O'Neill.