Apple said that if the EU's investigations concluded against Ireland, the company could be required to pay past taxes for up to 10 years "reflective of the disallowed state aid."
The EU began a formal investigation against Ireland in June last year for alleged state aid to Apple.
Apple said that as of March 28, it was unable to estimate the impact of having to pay these taxes.
"The company believes the European Commission's assertions are without merit," Apple said in a regulatory filing on Tuesday.
Back in October, the European Union accused Ireland of swerving international tax rules by letting Apple shelter profits worth tens of billions of dollars from revenue collectors in return for maintaining jobs.
European Competition Commissioner Joaquin Almunia had told the Dublin government in a letter published on Tuesday that tax deals agreed in 1991 and 2007 amounted to state aid and may have broken EU laws.
"The Commission is of the opinion that through those rulings the Irish authorities confer an advantage on Apple," Almunia wrote in the letter, which was dated June 11.
Apple said it had received no selective treatment. "We're subject to the same tax laws as the countless other companies who do business in Ireland," a spokesman said.
Apple, along with other multinationals, has found its arrangements scrutinised in recent years as corporate tax avoidance rose to the top of the political agenda in the United States and Europe.
Edited by NDTV staff from original story by Reuters