Britons travelling to Europe are facing fresh airport chaos as the EU’s new Entry/Exit System (EES) – an automated border check for non-EU nationals – comes into full force.

Since launching in April, EES has been linked to lengthy queues at airports, with some passengers even missing their flights.

And the disruption could now get worse.

The 29 countries using the system can currently pause checks during busy periods, helping to ease pressure during the peak summer season.

Greece, Portugal, Spain and France have all used the flexibility when needed.

But from Sunday, they will no longer be able to do so – raising fears of even longer queues for British holidaymakers. 

Several countries including Malta, Italy, Greece, France, Germany, Belgium, Portugal, Switzerland and the Netherlands wrote to Magnus Brunner, the Home Affairs Commissioner, in July and asked for the option to pause EES use to be kept after September 6, according to EuroWeekly News.

The full implementation could be delayed as the European Union is considering pushing back the final deadline, The Times reports. 

Apostolos Tzitzikostas, the European commissioner for sustainable transport and tourism, has apparently assured the UK privately that an extension is possible.

The new system has caused havoc all summer, and Ryanair boss Michael O’Leary has previously warned passengers that the airline “will not wait for anybody” caught up in lengthy queues. 

Speaking on The Telegraph's Travel Expert podcast, Mr O'Leary insisted: 'We will not wait for anybody, our priority is those passengers who are at the boarding gate when boarding starts.

'If you're not at the boarding gate when we finish boarding, the plane is going without you.'

As for what rights and protection passengers might have in such scenarios, Mr O'Leary said: 'You don't have any, which is regrettable but we're not delaying our flights for people who are stuck in passport control queues.'

Instead, he urged travellers to be prepared and arrive at the airport early.

'They have to show up at the airport earlier, but they have to be at the boarding gate otherwise they're not flying,' he said.

The travel boss identified airports including Lisbon, Madrid and Athens as 'particularly bad' for EES queues.

Mr O'Leary added: 'There are about 15 airports where there are real problems, two, three hour waits at border control which to my mind is unacceptable.'

Soon after the EES was fully rolled out, the budget Irish carrier wrote to the governments of all 29 countries and urged them to suspend the EES until September to help manage queues during the peak summer season.

Regarding Spain, which has been particularly affected by the system, Ryanair said: 'Despite knowing for over three years that the EES would be fully operational by April 10, 2026, Spanish authorities have failed to ensure adequate staffing, system readiness, or the installation of kiosks.' 

In Malaga, one British holidaymaker was left stranded in the hub with her daughter after missing her flight due to the long queues.

• READ MORE: Europe officially delays rollout of £17 ETIAS travel permit – again – as tourists are warned over scam visas