Airlines for Europe (A4E), the association that represents carriers such as British Airways, Ryanair and easyJet, said lengthy delays had been caused by many countries failing to provide enough staff for passport checks.
But the new rules mean checks against a series of databases are now carried out on each passenger from non-Schengen countries.
Some airports are already reporting delays of up to three to four hours at some airports, including Milan, Palma de Mallorca, Madrid, Lisbon, Lyon, Milan, Paris-Orly and others.
Airlines For Europe (A4E) said passengers arriving at airports in Spain, Portugal, France, Italy and Belgium are being forced to endure long waits to get through immigration.
European Union countries have to carry out tougher checks on passengers entering or leaving the Schengen area - which covers most of mainland Europe and lets people move passport-free. We're suffering like most other airlines.
The issue is compounded by a lack of border officials on the continent, it is claimed.
Passenger figures are up 4 per cent over the same weekend past year, with over 2,669 flights expected to arrive and depart between Friday and Monday.
"Member states must take the responsibility for this", A4E's managing editor Thomas Reynaert said.
"However, independent travellers will need to check the situation with their airlines and, where necessary, ensure they factor these longer queueing times into their travel plans when flying in and out of the airport".
"Aer Lingus guests travelling from Dublin Airport to the U.S. are being advised, via our social channels, aerlingus.com and via SMS, to arrive a minimum of three hours ahead of their scheduled departure to ensure the necessary time needed to complete U.S. pre-clearance before their flight", a spokeswoman said.
The scope and duration of such a temporary reintroduction of border control at the internal borders is limited in time and should be restricted to the bare minimum needed to respond to the threat in question.
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".
She wrote: "Mayhem at Barcelona airport, security queue stretching round whole airport and out exit!"
The firm said since July 24 around 1,000 passengers had not made their flights. Plane left most (sic) empty.