EES started to be rolled out in October last year and is now fully up and running.
The time it takes to register biometric information means people have been told to prepare for a wait at border controls.
During the introductory period, queues started to flare up at certain airports at busy times.
Since then, the system has been working well in some airports, while waits of several hours have been reported at others.
A representative of airline trade body IATA has warned queues in some places could be as long as six hours.
Travel experts and industry figures have blamed problems with the technology and border staffing levels. There have also been reports of people having to register their biometric information more than once.
The UK boss of Wizz Air told the BBC passengers should be prepared for a wait, and turn up three hours before their flight home.
Some passengers have missed flights home because the wait for EES checks meant they could not reach their gate in time.
Whether airlines will hold flights for passengers who get held up is a mixed picture. Some say they will wait wherever possible, while Ryanair is an example of a carrier which has said it will not.
