The FAI accounts for the year ending 2013 reveal debts of €50 million.
The figures were released ahead of the association's AGM on 26 July.
Overall income fell again to just over €36 million, representing a 19% drop over a two-year period.
There was €5 million spent on interest and other service charges on that debt.
The Republic of Ireland senior team begin their Euro 2016 campaign in September and those figures should crank up the pressure on side to qualify for the next major finals.
Giovanni Trapattoni's team secured a bonus of €8m by reaching the Euro 2012 finals, and FAI Chief Executive John Delaney will be hoping for a similar investment for the next European finals.
Delaney's stated goal for the FAI to be debt free by 2020 is now very much in question following the latest figures.
The chief executive's pay cut was also confirmed. He has dropped to earnings of €360,000, which constitutes a 10% pay cut on his 2012 salary.
Indeed, overall salary costs were down from €10.64m to €9.55m.
The FAI has said it is confident it will be able to repay the €50m debt.
A spokesman said the association has "guaranteed revenue streams that will enable us to continue to deliver on our football programme by repaying the debt.
"That includes a new television contract, the re-sale of premium seats and the re-sale of naming rights for the stadium, as well as UEFA funding."