Despite the U.S. criticizing the EU's decision, it is well aware that its own taxation rules have created an incentive for certain kinds of tax avoidance known as "inversions" - whereby firms have shifted their earnings to lower-tax countries in order to avoid higher U.S. taxes.
But Irish Finance Minister Noonan told CNBC that Ireland had not deliberately tried to attract U.S. companies for this reason and that the U.S. needed to sort out its own system.
"We don't invite U.S. companies to come to Ireland on the basis of inversion and we don't welcome them when they do, but under international law we cannot stop them … it is a matter for U.S. authorities to change the law," he said.
The U.S. announced earlier this year that it is looking to reform its taxation of international businesses, a move bound to keep corporate lawyers busy for some time. The commission's ruling was also likely to benefit the legal profession, with both Apple and Ireland set to contest the decision.
"The only certainty we know at this juncture is that there will be people getting rich off this: Lawyers," Neil Campling, senior vice president and head of global TMT research at Northern Trust Securities, told CNBC on Tuesday. "This will basically go through the courts for a number of years and there will be a number of legal issues that will come out of this," he said.