Travellers going through some European airports are reportedly waiting up to three hours at border checks because of the EU’s new entry-exit system (EES).

Passengers in airports in countries such as France, Germany, Belgium, Italy, Spain and Greece are waiting several hours at border checks, the Airports Council International (ACI) body has said.

Olivier Jankovec, the director of the ACI European division, told the Financial Times: “This situation, in the coming weeks and certainly over the peak summer months, is going to be simply unmanageable.

“We are seeing those queueing times now, at peak times, when traffic is just starting to build up.”

The EES came into effect on Friday in the Schengen countries – 25 of the EU’s 27 states plus Iceland, Liechtenstein, Norway and Switzerland. It requires passengers from non-EU countries, such as the UK, to register their personal information and biometrics at the border.

The system has been gradually introduced since October, and has already caused long delays at some airports. On Sunday the BBC reported that more than 100 passengers were unable to board an easyJet flight from Milan to Manchester before it took off because of delays at passport desks.

Airport representatives and the European Commission held a meeting to discuss problems with the system on Tuesday. The ACI is said to have asked to extend existing exemptions, as well as the power to fully suspend the new checks.

Jankovec told the FT that the ACI needed the ability to “fully suspend EES registration whenever there are excessive waiting times at border control that are just unmanageable”.

A spokesperson for the European Commission said: “What we can see from the first days of full operation is that the system is working very well. In the overwhelming majority of member states there are no issues.”

The commission said that the average registration of a passenger was 70 seconds, although the ACI has claimed that it can take up to five minutes.

The spokesperson said there were a “few member states where technical issues have been detected” but that they “are being addressed”.

They said: “It is up to member states to ensure the proper implementation of the EES on the ground.”

The spokesperson added that since the EES was introduced in October, it had registered more than 52m entries and exits, as well as more than 27,000 refusals of entry. Of those, almost 700 people were identified as posing a security threat.

In the run-up to Easter and before the EES was launched in full on 10 April, passengers crossing the Channel from the UK to France were told that they did not have to provide any biometric information because of delays in France’s developing the technology needed to collate and process the data.

Issues with the EES come as European airports also braced for potential jet fuel supply disruption caused by the blockade of the strait of Hormuz. On Friday the ACI wrote to the EU’s energy and transport commissioners predicting the bloc was three weeks away from systemic shortages.

Europe consumed about 1.6m barrels a day of jet fuel last year, of which roughly 500,000 were imported, according to the International Energy Agency, with about 75% coming from the Middle East.

Michael O’Leary, the chief executive of Europe’s biggest airline, Ryanair, has said the EES was causing queues of up to four hours at some airports, describing the system as “a shit show and a shambles” and a punishment for Brexit. He suggested that the EU should postpone the full introduction until October.