The Football Association of Ireland ordered the shredding of 18,000 match programmes containing comments from chief executive John Delaney about the FIFA crisis.
FAI chiefs confirmed that the programme for Saturday's Euro 2016 clash with Scotland had been re-printed at a reported cost of 10,000 euros.
A statement said: "John Delaney was entirely unaware of this change to the programme. He had already signed off on it and it was approved for printing.
"The decision to delete his comments where they related to FIFA was an editorial one that was taken by the communications department."
The FAI found itself dragged into the furore surrounding FIFA last week after Delaney confirmed the association had been paid five million euros by the governing body in the wake of Ireland's controversial World Cup play-off defeat by France in 2009.
The news came amid reports that a group of fans had clubbed together to hire a plane to trail a 'Delaney Out' banner over the Aviva Stadium during the game.
Inside the stadium, stewards moved in to remove an anti-Delaney banner when it was unfurled, while supporters in that section held up smaller cards bearing a similar message.