France, Belgium, Germany, Greece, Italy, Malta, the Netherlands, Portugal and Switzerland have not yet completely implemented the new controls.
For context, the EES was supposed to become fully operational in participating countries on September 6. But the aforementioned nine countries have asked for more time to fix technical issues and mitigate serious border congestion.
Meanwhile, Spain maintains EES checks at all of its external entry points.
Overall, the shift indicates that travelers must continue to undergo different procedures depending on their Schengen entry and exit points.
Why are countries delaying full EES checks?
The EES electronically records border crossings by non-EU nationals visiting the Schengen area for short stays.
Under the system, affected travelers provide passport information, fingerprints and a facial image. Their information is then stored electronically to help authorities monitor entries, exits and overstays.
However, the biometric requirements have created operational challenges at several European border crossings.
Some countries have experienced problems transferring biometric information to the central EES database. Elsewhere, border officers have struggled to retrieve existing traveler records.
Consequently, travelers have sometimes had to repeat the registration process.
France has confirmed that authorities will retain flexibility over EES implementation and pre-registration facilities until the end of 2026.
French ferry operators have also raised concerns about processing times.
At Granville, passengers arriving from the Channel Islands have faced waits of up to three hours after disembarking.
Therefore, authorities are trying to balance the new border requirements with the need to keep travelers moving.
EES implementation remains uneven across Europe
The delays do not mean the nine countries have abandoned EES.
Instead, biometric checks are already operating at many border crossings while others continue using limited procedures.
For example, fingerprinting has begun at Brussels’ Eurostar terminal and Antwerp port. Major hubs including Frankfurt and Amsterdam Schiphol are also collecting biometric information.
However, smaller airports have faced greater challenges.
EU sources cited by The Guardian said only 12 airports among approximately 1,500 border crossing points were still experiencing problems.
Meanwhile, the system has already recorded about 200 million registrations.
Authorities have also prevented around 70,000 people from entering the Schengen area, compared with 43,700 by June.
Those cases include travelers without required visas and people who exceeded their permitted stays.
Freight operators welcome EES flexibility
Concerns surrounding EES extend beyond airports and tourists.
Freight operators have warned that longer processing times could disrupt trade between the United Kingdom and European Union.
Logistics UK therefore welcomed the decision to maintain flexibility.
“The EU’s decision to adopt a pragmatic approach to the implementation of the Entry/Exit System (EES), to keep borders flowing, will come as a relief,” Chief Executive Ben Fletcher said.
The organization estimates almost 60% of UK-EU goods trade passes through the Short Straits.
Moreover, a 90-minute delay affecting 3.35 million heavy goods vehicle movements could cost the economy £400 million annually.
Logistics UK is consequently urging authorities to use the additional time to resolve technical problems and thoroughly test the system.
Gibraltar residents encounter separate EES problems
Recent cases involving Gibraltar residents have highlighted another challenge with the system.
Under current treaty arrangements, Gibraltar residents are exempt from EES registration when entering the Schengen area.
Nevertheless, some residents have been incorrectly registered at EU external borders.
In certain cases, EES recorded their entry into Schengen without recording a corresponding exit when they returned to Gibraltar.
As a result, the system’s 90-day counter continued running despite the travelers having already returned home.
The Gibraltar government has raised the problem with the European Commission.
Officials noted that the new exemption arrangements must reach approximately 1,500 external border crossing points across the Schengen area.
The government is also preparing guidance for residents affected by incorrect EES registrations.
What should travelers expect next?
Despite the latest delays, travelers should expect EES to remain part of European border procedures.
The system itself has not been suspended across the nine countries.
Instead, authorities have gained additional flexibility over how fully they conduct biometric checks while technical issues remain unresolved.
As a result, travelers could encounter different procedures between airports, ports and land borders.
Even within the same country, one crossing may collect full biometric information while another applies more limited checks.
France, for example, expects to retain flexibility through the end of 2026. However, no common new deadline has been announced for all nine countries.
Meanwhile, airlines, airports and border operators continue pushing for improvements before full enforcement.
For travelers, the practical message remains simple: EES is operational, but its implementation is still uneven across Europe.
Photo by Anthony Nelzin-Santos on Unsplash
