The European Parliament has approved a new electronic system to store biometric information on all non-EU citizens travelling in and out of the bloc – and post-Brexit, this could include British citizens.

The entry/exit system (EES) is part of the so-called Smart Borders package, and will consist of a central database storing the name, travel document, fingerprints, facial image, date and place of entry, exit and entry refusal of every third-country national – even visa-exempt travellers – coming to and from the EU Schengen area.

The data will be retained for at least three years – or five years for over-stayers – and will be accessible to border, visa and national enforcement authorities, as well as Europol, but not national asylum authorities.

The aim is to reduce irregular migration of over-stayers and fight organised crime, as well as speeding up border checks by replacing the manual stamping of passports. Data stored in the EES can be consulted to prevent, detect or investigate terrorist offences or other serious criminal offences.

Finnish MEP Jussi Halla-aho said: “Much of the data collected by the system could be vital in the fight against organised crime and terrorism – it’s crucial that national police forces and Europol will now have access to the data.”

But others have warned that such mass data collection is contrary to the EU Charter of Fundamental Rights and a recent court ruling.

“A few months ago, the European Court of Justice rejected the EU passenger data agreement with Canada,” said German MEP Cornelia Ernst.

That agreement envisaged storing similar data to the EES for up to five years. The court considered that holding onto such data for so long after the duration of a stay was an “interference with the fundamental right to respect for private life.”

“We are against this form of mass data retention from travellers. This will cost millions of euros and it is a shame for the European Union,” said Ernst.

French MEP Marie-Christine Vergiat said the scheme was originally intended to facilitate border crossing for the 50 million third-country nationals who come to the EU each year.

“However, this is now primarily a system for identifying people in irregular immigration situations and facilitating deportations,” she said.

“Under the false pretense of security, Europe is multiplying repressive forces’ access to sensitive data, including in cooperation with third countries like Sudan. Europe is turning into a bunker, undermining its own values and picking scapegoats for its problems rather than fulfilling our international responsibilities.”

Tanja Fajon MEP, a negotiator for the new system, was also worried about the implications for “bona fide travellers who pose no threat to the EU” and who should “not be seen as potential terrorists. We need to keep the balance between the purpose of this system and fundamental rights”.

The draft law had already been informally agreed with member states, and the European Commission is now pushing for it to be up and running “by 2020 at the latest”.