Finance Minister Michael Noonan has said that demanding €13bn in back taxes from Apple would be 'destroying the future for a short-term advantage.'
When quizzed by RTÉ, Noonan said that the European Commision's decision to order Ireland to demand back taxes from Apple could be detrimental to the country's economic future.
If the Irish Government win the appeal, Apple may not have to pay this bill.
However, Noonan maintains that appealing the decision is the best course of action.
He said: "It's my absolute judgment after examining all the factors that this is the best course of action. To do anything else would be like eating the seed potatoes and destroying the future for people for short-term advantage now."
Minister Noonan also indicated that a failed appeal could affect future European dealings with the US.
He said: "If an appeal were to fail and the money that's in an escrow account in Ireland was payable to the Irish exchequer, Apple would look for a tax credit and the ultimate losers would be the US exchequer.
"So you could look forward to serious disagreement between the US political authorities and the European commission in the future."
However, Noonan doesn't believe that this will affect future Irish investment from Apple.
"Apple have already committed to us that they will continue in Ireland, particularly in Cork, they're building a big data centre in Galway and that's on its way and they last week announced an extra thousand jobs for Cork so they're reinforcing their commitment to Ireland," he said.
When asked what would happen to the money, he added that it would remain in an escrow account until the appeal process is completed.
He said: "The revenue have a couple of months now to do their calculations. They'll have to enter into negotiations with Apple then to recover the amount. The amount must be recovered regardless of whether there is an appeal process or not and it will be put in an escrow account.
"The fact that Apple are appealing it means that, even if we never appeal, the money would be frozen or we would have the liability of repaying it in future years, if we were to spend it.
"The commision wearing another hat under their budgetary rules would require money like this to be taken off the national debt rather than being spent on day-to-day expenditure, but it would be a matter of the government of the future when the appeals process is completed."
The Government previously released a statement saying that they 'disagree profoundly with the Commission."