Europe’s aviation industry has warned that a new EU border control system could cause major travel disruption, with passengers potentially facing airport queues of up to four hours during the summer peak season.

In a joint statement released in Brussels, Airports Council International Europe (ACI EUROPE), Airlines for Europe (A4E) and the International Air Transport Association (IATA) said the Schengen Entry/Exit System (EES) is already producing significant delays and risks becoming unmanageable without urgent policy changes.

The groups said waiting times at airport border control points have already reached as much as two hours for some travellers as the system begins its phased rollout. Under the current stage, at least 35 per cent of all non-EU nationals entering the Schengen Area must be registered.

The organizations wrote to EU Commissioner for Internal Affairs and Migration Magnus Brunner, warning that three key problems are worsening the situation.

These include insufficient staffing at border posts, unresolved technological issues, particularly automated border systems, and the limited adoption of a Frontex pre-registration application designed to speed up checks.

They cautioned that if the system becomes fully mandatory during the busiest travel period in July and August, delays could extend to four hours or more.

The Entry/Exit System is a new biometric border control programme intended to modernise the Schengen Area’s migration management. Instead of passport stamps, non-EU visitors must register fingerprints and facial data digitally each time they enter or leave participating countries.

EU authorities say the system will improve security, track overstays and reduce identity fraud. However, industry groups argue the operational burden at airports has been underestimated.

“There is a complete disconnect between the perception of EU institutions that EES is working well and the reality experienced by travellers,” said Olivier Jankovec of ACI EUROPE, Ourania Georgoutsakou of A4E and Thomas Reynaert of IATA in a joint statement. They urged the EU to allow flexibility in implementation to prevent damage to Europe’s reputation as a travel destination.

Calls for Suspension Flexibility

The aviation bodies are asking the European Commission to confirm that Schengen member states can partially or fully suspend the system until at least October 2026. This is in case the operational pressures become too severe.

Under the current regulatory timetable, that flexibility may end as early as July, just before the summer travel surge when passenger traffic at major European airports typically doubles.

Airports and airlines fear that without the option to temporarily scale back checks, the system could overwhelm border control infrastructure.

If the warnings materialize, international passengers may need to arrive much earlier for flights and prepare for longer processing times at immigration. Travellers arriving from the UK, United States, Africa and Asia are most likely to be affected.

The issue is especially significant for British travellers. Since the UK left the European Union, UK passport holders are treated as third-country nationals under Schengen rules and are therefore subject to EES registration.

Travel industry observers say the rollout represents a broader tension between security modernisation and passenger convenience. While the EU seeks tighter migration monitoring and digital border management, airlines argue airports were not operationally prepared for the scale of biometric checks required.