The current investigation will try to establish whether Apple made a sweetheart deal with Irish authorities. A U.S. senator has already accused them of seeking "the Holy Grail of tax avoidance."
"We have received no selective treatment from Irish officials. Apple is subject to the same tax laws as scores of other international companies doing business in Ireland," an Apple spokesperson said.
"Apple pays every euro of every tax that we owe."
Pearse Doherty, finance spokesperson for opposition Irish party Sinn Fein, attacked the Irish government for its a "cozy" relationship with Apple and told CNBC the country risked "immense reputational damage" as a result of the investigation.
Taoiseach (Prime Minister) Enda Kenny's visit to California last week was overshadowed by the state's Governor Jerry Brown referring to Ireland's "creative accounting."
Fergal O'Brien, head of policy and chief economist at Irish business group Ibec, said he did not think investment in Ireland would suffer as a result of the EU investigation.
"This is an individual circumstance that doesn't have any read across to the rest of the Irish tax regime," he said.