In a 800 word letter Mr Cook accuses the European Commission of launching an effort to rewrite Apple’s history in Europe, ignoring Ireland’s tax laws and upending the international tax system.
He also highlighted the danger of the ruling to potentially hurt future investment and job creation in Europe.
However, the Apple CEO also took the time to emphasize Apple’s commitment to investing in Ireland and “serving our customers with the same level of passion and commitment”.
“As responsible corporate citizens, we are also proud of our contributions to local economies across Europe, and to communities everywhere.
“As our business has grown over the years, we have become the largest taxpayer in Ireland, the largest taxpayer in the United States, and the largest taxpayer in the world.”
Mr Cook also said he hoped and believed “the facts and the established legal principles upon which the EU was founded will ultimately prevail” in clearing the name of the multi-national company.
“We are confident that the Commission’s order will be reversed.
“At its root, the Commission’s case is not about how much Apple pays in taxes. It is about which government collects the money.
“Taxes for multinational companies are complex, yet a fundamental principle is recognized around the world: A company’s profits should be taxed in the country where the value is created. Apple, Ireland and the United States all agree on this principle.”
Mr Cook accused Brussels of taking unprecedented action, with serious and wide-reaching complications.
“Beyond the obvious targeting of Apple, the most profound and harmful effect of this ruling will be on investment and job creation in Europe,” he said.
“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 warned about how US multinationals and others will view the prospect of setting up shop on European soil if the retrospective multi-billion euro bill stands once several years of legal wrangling play out.
Mr Cook said: “It 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, and to the principle of certainty of law in Europe.”
And with Apple claiming it did not get a opportunity to defend itself during the watchdog’s investigation, Mr Cook went direct to customers.
“Taxes for multinational companies are complex, yet a fundamental principle is recognized around the world: A company’s profits should be taxed in the country where the value is created. Apple, Ireland and the United States all agree on this principle,” he said.
“In Apple’s case, nearly all of our research and development takes place in California, so the vast majority of our profits are taxed in the United States. European companies doing business in the US are taxed according to the same principle. But the Commission is now calling to retroactively change those rules.”