The budget airline said the decision is a political one that is not based on competition law.
The company said: "Ryanair ... was notified this (Tuesday) morning at a state-of-play meeting with the EU Commission, that the EU Commission intends to prohibit Ryanair's offer for Aer Lingus, despite the fact that Ryanair has met every competition concern raised in the EU's statement of objections and during the review process."
The EC said it would launch a detailed investigation into Ryanair's bid in August.
Ryanair, which currently owns just under 30% of Aer Lingus, has already attempted to gain control of Aer Lingus twice but ran into opposition from the EC and the Irish government on both occasions.
Last month it was told that it had one last chance to submit measures to ensure the proposed £591m merger did not reduce competition.
Ryanair's latest offer to the Commission included ceding 43 routes to Flybe and handing the routes operated by Aer Lingus from London's Gatwick Airport to British Airways.
A spokesman for EU competition chief Joaquin Almunia said: "The Commission will take a decision in this case at the end of February or the beginning of March."
He declined to comment further on the Ryanair statement.
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