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The EU has rejected calls by airports and airlines to suspend the implementation of new fingerprinting and facial recognition border controls even though it admits there are “20 difficult spots” with queue chaos.

With only a week to go before the peak summer holiday season starts, EU officials admit the new entry/exit system (EES) is “not perfect” but will tell travel industry representatives that a full suspension is “not needed” and “not possible”.

Under the EES, non-EU passengers have to register fingerprints and facial images the first time they enter the Schengen zone and then have their biometrics verified as they travel leave and re-enter.

Airlines and airport representatives and the International Air Transport Association (Iata) last week demanded a suspension of the new controls until next summer amid fears of chaos in holiday hotspots.

Iata said passengers were experiencing “delays and missed connections” in Portugal, Spain, Italy, Greeceand Belgium, while last week last week Ryanair warned last week of “queue chaos” in airports including popular holiday destinations such as Málaga, Alicante and Palma.

But EU officials say it is impossible to have the system open in some countries and not in others as it would lead to the “unfortunate situation of travellers stranded at border crossings”.

This could happen for example, if a passenger from Britain entered the Schengen area at a border where the new controls were operational but left via a border where they were not. In this instance they would be at risk of being registered as overstaying their 90-day travel allowance in any 180-day period and refused entry on a future trip.

The EU is also reportedly delaying the introduction of a separate pre-authorisation visa system known as European travel information and authorisation system (Etias), similar to the US Esta system, according to the Financial Times.

Officials said that out of the 1,500 border crossing points, only 20 were “difficult spots” and it would put pressure on those member states responsible to put measures in place to ease the pressure.

One of the sites with the worst delays was a small regional airport where 3,000 passengers arrived an hour and could not be assessed quickly because of space, officials revealed.

Lisbon had already eased its queues by deploying extra workers and 50 new Frontex border agency staff were being stood up in Brussels airport, officials said.

“I think we have recurrent progressive improvements everywhere,” an EU official added.

The controls have been eight years in the making and were designed to address weakness in border controls exposed by the terror attacks in Brussels and Paris in 2015 and 2016.

The introduction of system was delayed many times before it finally began last October, but with options for member states to opt out while the technology and the logistics of fingerprinting passengers were tested.

Under the new EES regulations, airports and ports can temporarily suspend the system if queues become unmanageable, but that opt-out is due to end in September.

So far “no member states have requested” a suspension beyond September, something the travel industry wants.

The EU, however, says the system is already bearing the results it was designed to achieve. It has captured 110m journeys in and out of the Schengen area, and about 44,500 people have been refused entry.

These include passengers trying to re-enter the bloc illegally either because they have overstayed a visitor allowance or because they were trying to enter on a second passport or false travel documents.

Previously a passenger with dual nationality, for example, could have beaten the 90-day visitor allowance in any one 180-day period by using their second passport. Under the new system fingerprinting or facial recognition can detect if they are overstayers.

EU officials revealed that the biggest reason for refused entry was “no appropriate justification of visit or stay”. The second biggest cohort of refusals, some 9,000, was people who had overstayed their 90-day visitor allowance.

More than 1,000 people were stopped at the border because they were “considered a threat to internal security”, while 300 were caught using false passports or travel documents.

Issues with French technology have been blamed for delays in full implementation of the system at Eurotunnel, which has invested £80m in infrastructure that is yet to be fully switched on.

Under the plans French border officials were due to have an iPad or tablet to hand to the driver and passengers to verify fingerprints and or facial images, but this has not yet been launched.

A time-saving mobile app developed by Frontex that would allow passengers to upload some data before they leave home is only fully operational in Sweden and partially in Portugal.