Apple has warned that future investment by multinationals in Europe could be hit after it was ordered to pay a record-breaking €13bn (£11bn) in back taxes to Ireland.

The world’s largest company was presented with the huge bill after the European commission ruled that a tax deal between Apple and the Irish tax authorities amounted to illegal state aid. The commission said the deal allowed Apple to pay a maximum tax rate of just 1%. In 2014, the tech firm paid tax at just 0.005%. The usual rate of corporation tax in Ireland is 12.5%.

“Member states cannot give tax benefits to selected companies – this is illegal under EU state aid rules,” said the European competition commissioner Margrethe Vestager.

In a letter to customers, Apple’s chief executive Tim Cook claimed the ruling could deal a blow to big companies investing in Europe: “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. He also said the commission was rewriting Apple’s record in Ireland, overriding Irish law and disrupting the international tax system. He said Apple chose the Irish city of Cork as its European base 30 years ago and had expanded from 60 workers to almost 6,000 in Ireland.

The Irish government also wants the ruling reversed because it can effect their low-tax base for overseas companies.

A cabinet meeting will be held in Dublin on Wednesday to discuss the fallout from the ruling.