Apple said it paid a total of $800 million (€718.6 million) of tax on European profits routed through its Irish entities in 2014, disputing a key element of the European Commission's case that it received selective tax advantage in Ireland.

The commission ordered Ireland to collect up to €13 billion in unpaid taxes, plus interest, from Apple for the period 2003-2014, after ruling that the iPhone maker received special Irish tax advantages that amounted to state aid.

According to EU competition commissioner Margrethe Vestage, this allowed Apple to pay an effective corporate tax rate of 1 per cent on its European profits in 2013, down to 0.005 per cent in 2014.

In a questions and answers document for investors published on Apple’s website on Wednesday morning, the company said the figure quoted by the commission were “extremely misleading and deceptive”.

“We paid $400 million in taxes in Ireland in 2014 – considerably more than the commission’s figure suggests,” Apple said. “We were certainly one of the largest corporate taxpayers in Ireland that year, if not the largest.”

In addition, Apple paid $400 million of current US taxes on those profits, bringing total current taxes paid to $800 million, it said.

“Most importantly, the commission completely ignores the fact that the vast majority of those profits was subject to US taxation,” Apple said.

The EU ruling appears to suggest that Apple’s main Irish-based company that’s responsible for selling its products in Europe only paid €10 million of corporate tax in 2014 - an effective tax rate of 0.005 per cent.

Both Apple and the Irish Government plan to appeal the EU's decision. The California-based group also said it expects it will have to place "a small amount of cash in an escrow account", pending the final outcome of the appeals process, which is likely to take several years.

Apple said it does not expect any near-term impact on its financial results or a restatement of previous earnings as a result of the decision.

“We have previously accrued US taxes related to the income in question,” it said, adding that it does not currently expect the EU ruling to impact its tax rate in future.

Shares in Apple fell 0.8 per cent to $106 on Wednesday in New York, giving the group a market capitalisation of $571.2 billion (€511.5 billion), as investors weighed the EU ruling against the company’s $230 billion-plus cash balance and the fact that the appeal process will take years.

However, other blue-chip technology stocks, including Microsoft, Facebook and Alphabet (the parent company of Google), all ended up declining as well.

“Globalisation has allowed multinational companies to base a large part of their operations in lower tax regimes. Indeed, many countries have openly courted big companies in the hope that investment and jobs would be higher as a result,” said Jim Reid, a macro strategist with Deutsche Bank.

“While corporate tax rates around the world have generally fallen, budget deficits have generally increased,” he said. “Although there are other reasons, lower corporate tax rates have not helped government finances.

“It does seem that in a world of low growth, high deficits, generally high corporate cash balances and low corporate tax rates, companies have been vulnerable to a change in the political wind,” Mr Reid said.

Meanwhile, Davy economist David McNamara said Apple’s change to its corporate structure last year may partially explain the surge in Irish corporation taxes in recent times.

When the Government moved in 2014 to close a loophole that allowed companies to be Irish-registered but not based anywhere for tax purposes, Apple closed the “stateless” arm of its Apple Sales International unit in Dublin, Mr McNamara said.

Last month the Irish Central Statistics Office raised its 2015 Irish gross domestic product growth estimate to 26 per cent, partly due to multinationals based in Ireland moving assets “onshore” in this country.

“Nevertheless, with much of the national accounts data redacted, we cannot be certain which multinationals drove the 26 per cent growth,” Mr McNamara said.