The so-called Entry/Exit System (EES), was supposed to kick in last November but was delayed at the last minute as several states were not ready.
First agreed on in 2017, the automated system will record visitors' date of entry and exit and keep track of overstays and refused entries.
Visitors to the bloc's Schengen free movement area will also have biometric data -- facial images and fingerprints -- collected at ports of entry.
READ ALSO: EU reveals how EES biometric border checks will be phased in
"The aim is to improve security, speed up the border check process, and reduce queues," the European Parliament said.
But some have raised fears that a rushed implementation could lead to longer waiting times for people travelling to Europe on trains, ferries and planes.
London's mayor Sadiq Khan warned last year it could trigger "chaos" at the British capital's Eurostar cross-Channel rail hub, St Pancras station.
READ ALSO: How can you prepare for travel under Europe's new EES and ETIAS rules
The UK, which left the European Union in 2020, this year launched its own digital travel permit, which is mandatory for European visitors.
Under the roll-out approved by European lawmakers in Strasbourg, with 572 votes in favour and 42 against, the EU scheme will be implemented over a six-month period.
The exact date is to be decided by the European Commission after the law is formally adopted and enters into force.
Member states would ramp up towards operating the EES system at half of border crossing points after three months and by six months countries should be registering all individuals using the system.
Emma Pearson
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