The new US custom and immigration pre-clearance facility in Shannon Airport is not being used by Aer Lingus for its transatlantic services.
The facility provided by the US, which opened three weeks ago, carries out customs, immigration and agricultural checks by US officials at the airport.
The three US carriers Delta, Continental and US Airways have signed up to use the facility.
An Aer Lingus spokeswoman said the decision was purely 'operational'.
As pre-clearance is not yet available on transatlantic flights from Dublin it was decided to 'keep the product consistent' from both airports.
Mayor of Shannon Sean McLoughlin has strongly criticised the Aer Lingus decision.
Minister of State Tony Killeen is to raise the issue with Aer Lingus.
