Rome’s airports will have to suspend the EU’s new digital border system for non-EU citizens to avoid a “disaster” during the peak tourism summer months, according to the head of the airports company.

Marco Troncone said that allowing passengers to skip the biometric entry-exit system (EES) was the only way of avoiding travel chaos over the summer amid warnings from other European airport officials.

Non-EU citizens, including Britons, must have their fingerprints and facial images taken the first time they enter the EU, under a new scheme designed to control EU borders.

The system was first introduced last October and fully rolled out in mid-April after delays, and has been delayed by faulty technology, leading to long queues for passengers even before the peak summer travel period, with some people missing flights.

“We are very worried for the summer,” Troncone, chief executive of Aeroporti di Roma, which operates Fiumicino and the smaller Ciampino airport, told the Financial Times.

On a scale of one to 10, he said his concern is now “eight or nine”. He added: “The process proves to be incompatible with the peak volumes that we are going to face. So the only way is to open up the valve. There is no way that we can deliver 100% of the enrolment.”

British travellers have faced huge delays in some countries and French police temporarily suspended the extra checks at the port of Dover in May. Greece has scrapped a previous promise to spare UK travellers from biometric checks until September.

Passengers who have passed through EES before and should be able to skip the queues are often forced to carry out the checks again.

Stefan Schulte, president of ACI Europe, Europe’s airports trade body, told the BBC earlier this week that individual EU governments had to decide whether to suspend the system, not airports. He said politicians should “stop pretending … that EES is working just fine. It is not.”

In early May, the European Commission referred to the “built-in flexibility” in the EES system that allows some functions to be suspended.

The airline industry group International Air Transport Association (Iata) has warned that queueing times could reach six hours in some airports over the summer, and that waits of up to three-and-a-half hours had already been recorded during peak periods.

“Two months in, [the system] is producing long lines, missed flights, and growing alarm across the travel industry,” Iata said last week.

Uku Särekanno, deputy executive director of the EU border agency Frontex, told an industry event in London this month that the situation may not “stabilise” for two years.