Duff slammed the FAI over the state of the game in the Republic of Ireland.
The former Chelsea stated: "I would - how would I word it - raze Abbotstown to the ground because it's the most uninviting, unenthusiastic workplace, not in world football but in the world.
"So I'd level it and I would probably sack 90% of the workforce."
However, Duff has now written a letter of apology for his words.
He stated: "I knew it was wrong when I said it and it is all I have thought about since.
"You are all working hard for the benefit of Irish football. Trying to pay bills, support families and pay mortgages and, frankly, it was a ridiculous comment.
"It was deeply disrespectful to you all and you all have every right to be disappointed and angry with me.
"I love Irish football, I love the league and will always continue to fight for them both but my words helped neither. My emotion and fight for the game came out poorly and I regret it."