The EU order said at the time that a number of deals that Apple had made with Irish authorities were illegal.
The EU published the full version of its ruling on Monday. It said that the Irish government had not offered any justification for the selective treatment meted out to Apple over its tax arrangements in Ireland.
When it issued the order in August, the EU competition commissioner Margrethe Vestager said Apple's "selective treatment" resulted in an effective tax rate of 1% on its European profits in 2003. This rate fell to 0.005% by 2014.
"Because our products and services are created, designed and engineered in the US, that's where we pay most of our tax... this case has never been about how much tax Apple pays, it's about where that tax is paid," the company said.
The Irish government said the European Commission's analysis was flawed and hence it was seeking annulment of the decision and had lodged an application with the General Court of the European Union.
"Ireland did not give favourable tax treatment to Apple – the full amount of tax was paid in this case and no State aid was provided. Ireland does not do deals with taxpayers," it said.