The accusation comes in a letter from the European Commission which was originally sent to the Irish government in June and was published online today.
The EC is currently looking at whether a number of countries, including Luxembourg and the Netherlands, unfairly favour large multinational companies.
Firms are often able to reduce their tax liabilities by channeling overseas sales or payments to use in-house brands or designs through subsidiaries.
In the letter, the European Commissioner Joaquin Almunia told Ireland: “The Commission’s preliminary view is that the tax ruling of 1990 (effectively agreed in 1991) and of 2007 in favour of the Apple group constitute state aid.”
Both Apple and the Irish Department of Finance deny the claim.
In a statement, the company said: “Our success in Europe and around the world is the result of hard work and innovation by our employees, not any special arrangements with the government.
“Apple has received no selective treatment from Irish officials over the years. We’re subject to the same tax laws as the countless other companies who do business in Ireland.”