The European Commission tried to "re-write" Irish tax law to make all Apple European profits taxable in Ireland, Finance Minister Paschal Donohoe insists.
He told the Dáil yesterday that there was 'no basis' for the Commission's 2016 decision, which would have obliged Apple to pay €13bn to the Irish Exchequer.
It had "misrepresented" the position of Irish law and the activity of Apple, Mr Donohoe said, and Ireland had thus a duty to appeal in its own right.
It was not a case of illegal State aid, as Commissioner Margrethe Verstager had ruled after a two year investigation, and the General Court of the European Union had struck it down, he said.
"This case did have a significant effect" on Ireland's reputation, the Minister said,
Mr Donohoe said that Ireland had not given a selective or special tax rate to any individual company and said there had been "mismatches" between the Irish and tax codes.
"There has been inappropriate and unfair labelling of our tax system, including by some members of this House because of our low tax rate," he said.
The decision of the court 'has fully justified our decision to appeal," he added.
In its decision, the General Court of the European Union ruled that as a matter of Irish tax law, Apple's intellectual property assets belonged at its headquarters in Cupertino, California and not in Ireland, and it said that as a result of that, the taxable profits of the Irish branches should have reflected their activities and not the entire activity of the multinational group.
However, the Court ruling also reaffirmed the right of the Commission to investigate tax laws and tax rulings under State aid law.
Sinn Féin spokesman on Finance Pearse Doherty said an Irish subsidiary of Apple had paid "an effective tax rate of 0.05pc for ten years".
He added that Ireland's "tax system is tarnished", warning that the European Court could well overturn the judgement on appeal.
It is not yet clear whether the Commission will appeal the ruling, although tax analysts say that any determination of aid would be well below €13bn sought in the original case, the largest brought under EU law.