The new EU border system that has triggered hours-long delays at big airports may not “stabilise” for two years, an official has warned.

Uku Särekanno, a director of the EU border agency Frontex, said some member states were “struggling” to adopt the entry/exit system (EES), which requires passengers from non-EU countries to register their personal information and biometrics at the border.

Särekannotold an event hosted by the UK travel association Abta: “We expect that the situation will stabilise in one or two years.

“The most challenging part is the first enrolment, that is the moment where fingerprints and facial images will be taken. If a person is visiting the EU again, they don’t have to go through the same process, so they can have a more fast track of entry.”

The EES was first introduced last October, before being rolled out in full on 10 April. EU rules allow the checks to be suspended to avoid queues at peak periods, though this allowance is expected to end in September.

There are fears that the checks could contribute to a summer of travel chaos in Europe, with consumers nervous over bookings and delays.

Särekanno said European member states ware “still adjusting to the new reality”.

“There are ones which are managing it rather well, who have dedicated resources,” he said. “There are the others who are still struggling. This adjustment … is taking some time and effort.”

In May, French police temporarily suspended the extra checks at the port of Dover. The Greek tourism minister, Olga Kefalogianni, told the BBC that Greece would suspend biometric checks for British travellers until September to prevent summer disruption.

British travellers have faced huge delays at border checks.

Mark Tanzer, the chief executive of Abta, said problems with the EES system could hurt demand among British holidaymakers this year.

“The rollout of the EU entry/exit system … is creating an unhelpful, and potentially damaging, backdrop for summer travel to EU destinations,” he said. “There clearly are some hotspots, and we urge destinations to use the contingency flexibility allowed under the regulation to suspend the biometric registration where queues are unacceptably long.”

He added that holiday bookings for early summer had also been hit by uncertainty around the conflict in the Middle East and the rising cost of living.

“There is evidence from our research that apprehension generally, and the rising cost of living here, are dampening early-season booking levels,” he said

Consumers are increasingly booking their holidays later in the year, amid fears around the impact of the conflict in the Middle East on travel. The war has triggered a rise in global oil prices, with jet fuel costs jumping even more sharply and bringing the prospect of higher air fares. However, large numbers of flights have not been cancelled during the lucrative summer holiday season, as had been feared.

Shaun Morton, chief executive of the holiday operator On the Beach, also speaking at the Abta conference, said that while bookings had been coming in, shorter lead times “creates uncertainty and makes planning difficult”.

“We have a price-sensitive and uncertain consumer who was already booking on a later booking curve, who is now also concerned about coming out of this war – more inflation, fuel shortages and fuel surcharges,” he said.

However, he still expected the summer travel market to grow overall this year. “This late loop will eventually reverse when the conditions allow it to,” Morton said. “This is cyclical … where people do miss out on their holiday this year, I’m sure they will make sure they don’t miss out on it next year.”

Shares in On the Beach have fallen 30% this year, including a sharp drop last month, when the group warned that holidaymakers were booking later this year.