Airlines For Europe, which represents carriers including easyJet, Ryanair and British Airways' parent company IAG, claimed some passengers are even missing their flights because of the issue.
The airline said due to recent "enhanced security measures" by the US Department of Homeland Security, Aer Lingus passengers are "experiencing delays" at US Customs Border Protection at Dublin Airport.
Airlines For Europe, a group which represents carriers including easyJet, Ryanair and British Airways' owner IAG, said that compared to a year ago some delays had increased by 300 per cent and that some passengers had missed flights.
Managing director Thomas Reynaert said: "Travellers face long lines and can't get on their flights".
New border controls have left some holidaymakers queuing for up to four hours at Europe's main airports.
"While border arrangements for Schengen countries are not in the United Kingdom government's control, I will be speaking to my counterparts in Portugal, Spain and Italy to urge them to do all they can to reduce queues and allow travellers to get on with their holidays".
The statement points specifically to airports in Spain, France, Italy, Belgium and Portugal.
This has taken up to two minutes per passenger which has led to delays.
"However, independent travellers will need to check the situation with their airlines and, where necessary, ensure they factor these longer queuing times into their travel plans when flying in and out of the airport".
She wrote: "Mayhem at Barcelona airport, security queue stretching round whole airport and out exit!"
The European Commission that it was up to EU member states to ensure that rules are implemented, and that the delays were "the price of security".
The delays are reportedly being caused by the introduction of newly-toughened and more time consuming immigration checks.
She said it was the responsibility of member states to provide enough resources to make the checks "as smooth as possible", adding it was "very clear that member states had time to prepare".