Apple has furiously rejected charges from Brussels that it should pay €13 billion in unpaid Irish taxes, accusing the European Commission of ignoring decades of laws in ordering Ireland to recoup the money.

The iPhone maker on Monday lodged a formal appeal against the Commission's claim that illegal sweetheart deals with the Irish government constituted state aid and allowed Apple to pay a fraction of what it owed over more than a decade.

The company claims that the Commission had investigated the case with a political agenda, that Apple has been singled out for special treatment, and that its decision flies in the face of international tax laws.

The appeal adds to a separate challenge from the Irish government, and marks the latest step in a long-running dispute with Brussels, which has sparked transatlantic tensions with Washington.

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"It's been clear since the start of this case there was a pre-determined outcome," Apple said.

"The Commission took unilateral action and retroactively changed the rules, disregarding decades of Irish tax law, US tax law, as well as global consensus on tax policy, that everyone has relied on.

"If their opinion is allowed to stand, Apple would pay 40 per cent of all the corporate income tax collected in Ireland, which is unprecedented and, far from levelling the playing field, selectively targets Apple. This has no basis in fact or law and we're confident the ruling will be overturned."

The Commission has published an exhaustive 130-page document outlining its decision in August to charge Ireland with illegal state aid, which it says allowed Apple to pay corporation tax of as little as 0.005 per cent on its profits in Europe and elsewhere from 2003 to 2014.

It said the corporate structure Apple employs in Ireland, which sees profits assigned to a subsidiary without any staff or tax residence, does not correspond to economic reality, and so rulings made by the Irish revenue in 1991 and 2007 around the company's structure break EU laws on giving companies special deals.

Apple says that the billions of dollars it routes through Ireland should be taxed in the US, where its research and development takes place, and denies that its structure is the result of special arrangements.

"Because our products and services are created, designed and engineered in the US, that's where we pay most of our tax. We've long advocated for tax reform with a simple, straightforward system, but this case has never been about how much tax Apple pays, it's about where that tax is paid," it said.

The Irish government, meanwhile, says the Commission is overextending itself by imposing its view of tax laws onto the state aid case.

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The case will now be heard in the EU's general court in Luxembourg, a legal battle that may take years. Apple will pay the money to the Irish government this year but it will be held in escrow while the dispute is resolved.

A similar case involving Starbucks and the Netherlands over alleged sweetheart deals is also being appealed, while the Commission is also investigating the arrangements of McDonald's and Amazon in Luxembourg.

The Commission said it would defend its decision in court.