The number of people who missed flight connections in Europe doubled over the summer after the rollout of the region’s much-criticised electronic border system, airlines have said. Some carriers reported a sixfold rise in the number of passengers who failed to make connecting flights after being held up in queues that stretched for several hours, industry body Iata said on Thursday. The industry had warned that the EU’s new Entry-Exit System, which requires non-EU passengers entering and leaving the bloc to take a photo and provide fingerprints, would cause long delays. “People missing flights is not new, but EES just makes it worse,” said Thomas Reynaert, a senior vice-president at Iata.

The smart border system was rolled out in full earlier this year but has been beset by problems including faulty technology and insufficient staffing levels, leading to long delays and warnings of summer travel chaos. To handle queues at peak times, some EU countries suspended parts of the checks over summer, only registering travellers’ personal details without their fingerprints or photo. This meant that the industry’s previous warnings of six-hour queues did not come to pass but there were still pockets of disruption across the region. “Even with the flexibility in place, we’ve seen that operational challenges continue to emerge across multiple border crossings in Europe,” Reynaert said.

European Commission spokesperson Markus Lammert insisted earlier this week that “the system has broadly worked well, also thanks to the flexibilities that are in the system”. This flexibility is due to be lifted at the end of this week, although the Commission has signalled that it would turn a blind eye to countries that continue suspending some of the biometric checks to handle surges. Airports such as Corfu and Tenerife were particularly affected during the holiday season, but officials believe the situation will become more manageable as summer ends.

Reynaert on Thursday warned that removing the flexibility “creates a real risk of increased congestion and disruption”. Lammert said the Commission had “offered additional help to the member states concerned and asked them to further intensify the operational preparedness, including the necessary technical, organisational and communication measures with a view to ensuring that remaining challenges are fully addressed by the end of the year”. EU officials have also said the Commission would not start procedures on legal breaches for the countries concerned. “There’s a strong joint will to make the system work everywhere in line with the rules,” Lammert said.

The Commission has also highlighted the benefits of the digital border system, which has registered 180mn entries and exits and refused 60,000 entries, including more than 1,700 people who posed a security threat.