The Irish finance department said it has given a detailed response, saying an EU ruling was not imminent.
"There is simply no question that the Irish authorities sought to give the company in question any kind of special tax deal," a finance department spokesman said.
Apple's vice-president of its European operations, Cathy Kearney, told a European Parliament hearing on Tuesday that the company had paid every cent of its taxes in Ireland.
The Commission has been investigating a string of multinationals over their tax arrangements with countries within the trade bloc.
Last year it ordered Fiat and Starbucks to pay back millions of pounds in taxes after ruling that some of their deals fell foul of state aid rules.
