It will be the first time in 52 years that transatlantic flights will not operate from the historical and traditional stopover route of Shannon.
Regrettably Aer Lingus has lost over $200million on its Shannon transatlantic winter flights for the last 15 years.
Aer Lingus chief executive Christoph Mueller said the airline remained committed to Shannon but they could not incur further losses on their winter routes.
"However, in order to maintain the viability of our Shannon transatlantic operations throughout the remainder of the year, the three-month suspension of these routes, when seasonal demand is at its lowest, is crucial,” said Mueller.
Almost 1,300 people have already booked transatlantic flights from Shannon during the suspended period. An Aer Lingus spokesperson said that customers were being offered a refund or an alternative flight.
Aer Lingus's decision will affect 270 staff at Shannon airport, who will be asked to take unpaid leave or work a shorter week.
Aer Lingus has declared that its transatlantic services from Dublin airport will not be affected.
A spokesperson for the Minister for Transport Noel Dempsey said, "The Minister welcomes the fact that Aer Lingus has reiterated its commitment to the Shannon market.
“He regrets very much the decision to suspend flights for 11 weeks, but he is satisfied from a meeting he had with Aer Lingus today that it is maintaining employment at Shannon.”
"Continental [to Newark, New Jersey] and Delta [to JFK, New York] have both confirmed that they will fly from Shannon this winter, yet our national carrier has decided to abandon the base,” said Breen.
“I think it’s sad that people in the region won’t be able to fly into New York or Boston for St Patrick’s Day with Aer Lingus.”
The Shannon region is being hit hard by the recession, new unemployment figures show that the number of unemployed has risen in the west and the whole of Ireland.
Chairman of the Irish Hotels Federation for the mid west region, Michael Vaughan said, "I’m disappointed but it’s not surprising."
“It’s the most difficult time of the year and has proved extremely hard to generate business.”