The EU has pushed back on complaints from some of Europe’s aviation heavyweights, including IATA, about the new EES border control system which is causing delays across Europe.
In a letter, EU Commissioner Magnus Brunner described the long-term benefits of the EES as “significant”.
The EES, which came into full effect in April, requires travellers entering the Schengen area to register fingerprints, photos and passport details through self-service kiosks. It applies across 29 Schengen countries, which allow passport-free movement between member states. The new system has reportedly led to severe delays across Europe this summer.
“Queues to access EES self-service kiosks are long. Be prepared to stand for an extended time. Take food and water if needed,” the Department of Foreign Affairs and Trade said in a statement.
Despite the criticism, the EU Commissioner has stuck by the EES.
“Europe’s security must be our common overriding priority,” Brunner said in a letter obtained by POLITICO.
So far, there have been nearly 110 million entries and exits registered under the new system, he said. This included 44,000 refusals of entry with 1,100 of those refusals identified as a security risk, he revealed.
Nearly a decade to prepare
Brunner pushed back on complaints made by the three aviation heavyweights, noting that “member states and the relevant players had nearly a decade to prepare for the arrival of the EES.”
Directly addressing wait times, Brunner said “the EES rules already anticipated initial adaptation challenges and, therefore, allow for maximum flexibility during the 2026 summer holiday period (until early September).
“Member states can suspend the registration of biometrics,” he added. This means that borders only have to register passports, effectively reducing process times to those before EES.
“This seems to suggest that other factors – unrelated to EES – like insufficient staff or a lack of adequate infrastructure, could be at the origin of delays especially at airports where no biometrics are registered.”
Despite the pushback, Brunner did recognise the “short-term” difficulties and pledged to make “additional efforts” to help member states struggling under the new system.
“The Commission has already started to facilitate the deployment of Frontex personnel in those Member States that would like to receive additional support”.

Delays have reached a critical point
Brunner was responding to a letter from Ourania Georgoutsakou, managing director of Airlines for Europe (A4E); Olivier Jankovec, ACI Europe director general; and Thomas Reynaert, senior vice president of External Affairs at IATA.
In the original letter, Georgoutsakou, Jankovec and Reynaert said they had “reached a critical point” in the management of the new system across Europe.
“The current implementation of the EES is creating severe operational consequences disrupting passengers and putting border authorities, airports and airlines under unsustainable pressure.”
The letter called for the EU’s “immediate intervention” to tackle the wait times which have reached 5 hours during peak times, it said.
Specifically, it called on the EU to “immediately provide Member States with all the flexibility needed to completely suspend EES, preventively whenever passenger volumes exceed the operational capacity of border control facilities, at least throughout July and August,” and to “establish by September a permanent operational flexibility mechanism allowing Border Control Authorities to suspend EES procedures under clearly defined exceptional circumstances.”
The trio also said they were “deeply concerned” by comments made to the Financial Times in which a spokesperson for the European Commission said the EES was fully operational and working well. The spokesperson also said that the delays were not owing to EES but were due to pre-existing factors such as concentration of flights in specific slots.
At the end of his letter, Brunner said he is looking forward to a meeting to be held on the 7 July.
