The Government has been accused of bias against the FAI after refusing to allay costs of £250,000 incurred in the Euro 2000 fixtures chaos caused by the Balkans crisis.
The association had sought a "gesture of support" in the wake of the irrecoverable losses sustained by the postponement of three senior and three under-21 European Championship fixtures.
They claimed they were victims of what was essentially a political situation, and that the Government had exacerbated the problem by refusing to grant visas to the Yugoslav squad for the game scheduled for Lansdowne Road last June.
Apart from the £100,000 spent on installing temporary seating for the fixture, the FAI was fined by UEFA and ordered to contribute £50,000 towards the expenditure incurred by the Yugoslavs.
FAI officials were said to be enraged by the curt note of rejection from Minister for Finance Charlie McCreevy and they suggested it was further evidence that, in comparison with other sporting bodies, the association is disadvantaged in its dealings with Government.
"Football in this country is largely dependant on the voluntary element," said the FAI's chief executive, Bernard O'Byrne. "There are anything up to 400,000 people involved in promoting and fostering the game and they need to be reassured that people in government are not actively disadvantaging them.
"I would hope not, but I have to say that I am both worried and frustrated by what I perceive as shabby treatment in our dealings of late with the Government.
"For example, we presented them with a pre-Budget submission for funding for a thoroughly researched and perfectly viable five-year plan to help some of those people who feel socially excluded. I am mystified why we didn't even get an acknowledgement, let alone a positive response to our document.
"Again, in the annual list of sports grants on Tuesday we were awarded £114,000, or roughly the same figure as we got last year. In the context of what we're about this is wholly inadequate, and the word derisory was one that kept coming back to me yesterday from our people on the ground.
"When you put it all together there is indeed justification for people asking if there is an agenda against the FAI, and if so why."
After a century of antagonism between those who administer Irish football and successive generations of GAA officials, both of the main players in the Irish sporting arena are anxious to be seen to have distanced themselves from at least some of the issues which separated them in the past.
Yet, in the midst of that faintly discernible move towards ecumenism, the suspicion among the soccer fraternity is that politicians still find it more expedient to align themselves with Jones's Road rather than Merrion Square.
O'Byrne, anxious not to be seen as disturbing the fragile peace, was choosing his words carefully when he said: "We don't begrudge other organisations their good fortune in securing State funding, but from our perspective it's difficult to escape the conclusion that we're being shabbily treated."
For some time now the perception among the wider sporting public is that of a deteriorating relationship between senior Government ministers and the FAI in the wake of the soccer body's decision to press ahead with plans to build their own stadium at a time when the Taoiseach, Bertie Ahern, was promoting the concept of a national stadium.
Ahern, a Dublin northsider who would be seen as having more in common with soccer than Gaelic games, still believes that pragmatism demands the construction of a national sporting arena rather than one funded by an individual organisation.
That is a view which the FAI, driven by the visionary instincts of O'Byrne and others, finds difficult to accept. In spite of the sound financial base of their strategy, the danger for Government is that in the current climate of mutual distrust they risk being perceived as petty.