The new rules, which must be rolled out across the EU's passport-free Schengen zone by October 7, mean passenger details of non-members are run through a database to alert authorities if they are known to pose a threat.
The problem - at what is traditionally already the busiest time of the year for flights - is being made worse by a lack of border officials on the continent, it is claimed.
The details of people from non-Schengen countries, such as the United Kingdom, will be run through databases to see if they pose a threat.
Just 78% of the Dublin-based carrier's flights were on time on Tuesday, down from 90% during the month of August as a whole past year.
Thousands of British holidaymakers are facing hours of extra-long security queues because of tougher European Union border checks.
Passengers arriving at airports in Spain, Portugal, France, Italy and Belgium are being forced to stand in immigration lines for "up to four hours".
British holidaymakers have reportedly been stuck in airport queues of up to four hours following the introduction of stricter border controls around the EU.
Managing director Thomas Reynaert said: "Travellers face long lines and can't get on their flights".
Many travellers said they were unaware of the long queues and the extra time needed to get through some airports.
People are being warned to check what terminal they are flying from, arrive in plenty of time for their flights and to expect large crowds in the airport.
Irish passengers face delays overseas because their details must be run through new databases at passport control booths at airports and sea ports, to see if they pose a threat.
Border check points should be kept "sufficiently resourced" to keep queuing times as short as possible, she added.
"The implementation of the new rules falls under the responsibility of the member states who need to ensure the deployment of sufficient resources and also staff in order to make these checks as smooth as possible".
"More checks can lead to more delays, and that is the price for security". Phil Davis, whose flight home from Frankfurt yesterday was delayed by 90 minutes, said the airport only had one security lane open to process a large number of global flights.
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