BRUSSELS — The EU’s new digital entry system is now fully mandatory, but airport groups warn long lines are causing passengers to miss flights.

The Entry/Exit System is designed to replace passport stamps and curb overstays in the Schengen area. It requires non-EU travelers to register fingerprints and a facial image the first time they cross the bloc’s borders for a short stay.

The system was rolled out in phases starting in October before becoming fully operational on Friday.

Data collected by airport lobby ACI Europe across 15 countries shows that since Friday, “queues are now typically averaging two to three hours or even longer during peak traffic periods,” lobby chief Olivier Jankovec said on Tuesday.

“With traffic volumes set to rise further in the coming weeks and months, as is customary during the summer season, we are deeply concerned about the situation worsening and becoming unmanageable,” he added.

ACI wants border control authorities to make it easier to suspend the system if waiting times get too long.

But the Commission disputes that there is a big problem, and says countries should fully staff border control to prevent delays.

“It is up to Member States to ensure the proper implementation of the EES on the ground,” said Markus Lammert, the Commission’s spokesperson for internal affairs.

Airports across the continent are reporting problems.

Stefano Paoloni, secretary-general of Italy’s Autonomous Police Union, said lines at Rome’s Fiumicino Airport over the weekend occasionally extended “outside the terminal building.”

ACI and the Airlines for Europe lobby said on Friday that one flight to the U.K. “was missing 51 passengers at departure,” while other flights also had problems.

On Sunday, a Milan to Manchester flight departed while over 100 of its booked passengers were stuck in an EES queue, The Independent reported.

The EES is supposed to be quick, allowing people to upload their biometric data through self-service kiosks at border points. The European Commission said registering a passenger typically takes about 70 seconds.

However, that is only the processing time, while at many airports passengers are stuck in long lines before they get to a scanning booth or see a border agent.

But Paolini said he talked to border agent colleagues who are manually entering data, making the process even slower.

Three airport officials, speaking of being granted anonymity, said the EES was paused at several Italian airports on Friday morning after the system “went down.” One of the representatives said the problems continued into Monday.

The Italian ministry of internal affairs did not respond to a request for comment.

Three airports in Portugal halted collection of biometric data over the weekend to prevent passengers from missing their flights. Belgium also paused the collection of biometric data.

Countries can also introduce a dedicated app to speed up the process, but it’s currently only available to use for uploading data when entering Sweden. When entering Portugal, the app can be used but only to fill in a questionnaire.

Despite the complaints about disruptions, the Commission’s Lammert said the EES has registered over 52 million entries and exits and 27,000 refusals of entry, “of which almost 700 persons were identified as posing a security threat to the Union.”