The first British and other non-EU citizens will be subjected to new biometric checks when travelling to Europe from Sunday, when the long-delayed entry-exit system (EES) is finally launched.

However, a phased implementation to avoid chaos at borders means it could be another six months before every traveller is checked, with passport stamping continuing until the system is fully up and running.

Under EES, most non-EU or non-European Economic Area citizens or residents will be photographed and have their fingerprints scanned at the border to travel into the Schengen area.

Travellers will need to scan their passport and may also be asked to confirm whether they have accommodation, a return ticket, sufficient funds and travel/medical insurance – although not all border crossings will demand this.

Banks of new machines have been installed at airports and borders around Europe in anticipation of the system, whose start date was originally scheduled for 2022.

Cross-Channel departure points where the French and EU border is on UK soil, including Eurostar at St Pancras international train station, have invested tens of millions of pounds in infrastructure and computer systems to comply with the new requirements.

The time needed for additional checks – especially for drivers and passengers who will need to leave their vehicle to register information – has led to fears of long queues, particularly at the Port of Dover ferry port, and to a lesser extent at Eurotunnel at Folkestone.

Two overflow sites in Kent for motorway traffic have been secured by the government in case of tailbacks.

However, fears of gridlock have been largely abated due to the phased rollout. Only coaches and HGVs will be checked for the first month at Eurotunnel and Dover, and only a minority of passengers requested to register at Eurostar until January.

The European Commission said on Friday it expected the system would mean “travelling will become smoother and safer for all” with databases automatically giving border officials across the EU instant access to irregularities.

During the progressive rollout, EU member states will be able to decide at which border crossing points they will start deploying the system, and when. It would allow them to “start benefiting from the new system, while ensuring that border authorities, the transport industry and travellers can adjust to the new procedures,” the commission said.

The UK government is expected to remain in close contact with EU authorities to monitor its introduction and has launched an information campaign for travellers. While it said checks should only take up to two minutes for each person, it warned they could face longer waits on arrival in the Schengen area.

Keir Mather, a UK transport minister, said: “Our priority is to minimise disruption for travellers and hauliers, particularly at our busiest border crossings.

“We’ll continue working closely with European partners and local resilience forums to keep traffic flowing and journeys smooth.”

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According to recent research by the travel organisation Abta, almost half of all Britons and 39% of regular travellers remain unaware of the EES requirements.

It is believed that many British expats have avoided detection when outstaying the post-Brexit 90-day limit for visits within a 180-day period. An Abta spokesperson said: “It should eventually make travel easier. But those breaching the 90-day rule will be automatically detected.”

The freight industry has urged the government to secure an exemption for professional drivers, who may also have been waved through the border until now.

Trade body Logistics UK welcomed the phased introduction but said “disruption was inevitable”, and called on the government to work with France to develop an app to allow drivers to register away from the border.

The EU expects passport stamping to be phased out before 10 April ahead of the busy summer travel period, with travellers advised to go to the official website if they are unsure of requirements.

EES requirements will apply to countries in the Schengen area, which include non-EU Iceland, Norway and Switzerland, but not Ireland and Cyprus.