Cook said in a statement that Apple "received guidance from Irish tax authorities on how to comply correctly with Irish tax law" and "Apple follows the law and we pay all the taxes we owe."
Both Ireland and Apple are appealing the decision. Cook said his company is “confident” the order “will be reversed”.
"This claim has no basis in fact or in law. We never asked for, nor did we receive, any special deals," Cook stressed.
"We now find ourselves in the unusual position of being ordered to retroactively pay additional taxes to a government that says we don't owe them any more than we've already paid," he added.
Shortly after Cook's comments, European Commissioner for Competition Margrethe Vestager said in an interview with MarketWatch that the EU has a solid case to defend any appeal attempt.
"We have of course structured the case in a way that it’ll be upheld if it goes to court. That’s why it sometimes takes a long time to finish these investigations," she said.
"This probe has been three years under way to make sure we really have a solid case, which I firmly believe we do,” she added.
Cook reminded in a statement that Apple began its operations in Cork, Ireland in 1980, and the company brought investment and employment to both the region and Europe since then, employing some 6,000 people across Ireland and around 1.5 million jobs across the continent.
“Beyond the obvious targeting of Apple, the most profound and harmful effect of this ruling will be on investment and job creation in Europe. Using the Commission’s theory, every company in Ireland and across Europe is suddenly at risk of being subjected to taxes under laws that never existed,” he said.
The CEO emphasized that the EU's decision could also have serious implications towards the nexus between supranational authority and government rule within the EU.
“[The Commission] is effectively proposing to replace Irish tax laws with a view of what the Commission thinks the law should have been. This would strike a devastating blow to the sovereignty of EU member states over their own tax matters," he explained.