Ryanair and the boss of Berlin Airport have warned of severe disruption to summer travel because of the new digital EU border check system.

Ryanair said families could face “queue chaos” and urged governments to postpone the system until after the summer holiday period.

Berlin Airport’s Aletta von Massenbach said non-EU nationals were having to queue for up to two hours under the new system, and warned the situation is “not bearable over the summer”.

Under the EU’s Entry-Exit System (EES) travellers from outside the bloc must register biometric information when entering most European countries, which is checked when they leave. The European Commission (EC) says it is willing to offer more support.

Von Massenback told the BBC’s Today programme that at one terminal in Berlin, where Ryanair and Wizz Air operate, waiting times can run between “an hour to two hours”.

Ryanair’s chief operations officer, Neal McMahon, said, external: “Passengers and families should not be used as guinea pigs for a half-baked passport control system that risks creating long queues, missed flights and unnecessary stress at airports this summer.”

The airline said airports such as Tenerife South, Palma, Alicante, Malaga, Milan Bergamo, Krakow and Paris Beauvais were experiencing major disruptions.

Last week, the head of Europe’s airports trade body said worries over the EES were keeping him and other industry bosses awake at night.

The EES is meant to modernise the EU’s system of border control, making it more secure and eventually making travel smoother.

It has been fully operational since April. While the system has worked fine in some places, there have been regular reports of long waits at passport control, especially at peak times.

Some passengers say they have missed flights home because they’ve been held up in queues.

Von Massenbach said one issue was that EU countries used different systems.

“There are so many sub-systems for each and every member state,” she told the BBC. “We see that the complexity doesn’t really support smooth processing at the border.”

Technology issues have prevented EES from being used in the UK at the Port of Dover where French border checks take place.

A new processing area has 84 kiosks to record fingerprints and photographs but currently is not being used because the technology for the kiosks – the responsibility of the French authorities – cannot be activated.

Port of Dover chief executive, Doug Bannister, told MPs on Thursday “time is rapidly running out” to fix it.

“We are rapidly heading towards the start of the critical summer period and are yet to receive the assurances we need to avoid what has the potential to be a very challenging six weeks,” he said.