British holidaymakers travelling through Spain this summer have been warned they could miss their flights if they get stuck in long queues caused by the EU’s new Entry/Exit System (EES).

Airlines including Ryanair and Wizz Air have made clear that flights will not be delayed for passengers who fail to reach the boarding gate on time because of passport control hold-ups.

The warning comes as the International Air Transport Association (IATA) raised concerns that the new border system could create significant delays at airports across Europe.

Under the EES, non-EU travellers, including British citizens, will have their fingerprints and photograph recorded when entering the Schengen Area. The biometric data will then be checked again when they leave.

Rafael Schvartzman, IATA’s Vice President for Europe, said some airports are still not fully prepared for the introduction of the system.

‘What we are seeing is a very hard risk of really challenging waiting times,’ he said, warning that queues of three, four, five or even six hours could occur at some airports.

According to IATA, processing a passenger currently takes between 20 and 25 seconds, but this could rise to around 90 seconds under the new system, creating major bottlenecks during busy travel periods.

Ryanair boss Michael O’Leary has warned passengers not to expect airlines to hold departures for people stuck in passport queues.

‘Ryanair takes every passenger that is in the boarding gate when boarding closes,’ he said.

‘Passengers miss their flight not because we’ve left them behind but because they are stuck in somebody else’s passport queue.’

As a result, airlines are advising passengers travelling back to the UK to arrive at airports at least three hours before departure.

Concerns about the system have already been fuelled by several incidents linked to border control delays.

During Easter, more than 100 passengers were reportedly left behind at Milan Linate Airport after waiting around three hours to clear passport checks.

Last month, a Ryanair flight from Toulouse to London departed without around 150 passengers who were delayed by queues associated with the EES process.

The system has attracted criticism from some airline executives, with O’Leary previously describing it as a ‘punishment for Brexit’ because it will apply to UK travellers entering and leaving the Schengen Area.