The EU Entry-Exit System (EES), which requires non-EU citizens travelling to the union to submit to a facial scan and have their fingerprints taken, went live in October and is due to be rolled out at all external EU border crossings by mid-April.
However, Portugal's ministry of internal administration has confirmed the government has stepped in and halted the checks owing to recent long delays at Portugal's main airport.
The ministry said the pause was necessary to "implement and reinforce" contingency measures at Humberto Delgado airport, including increasing electronic and physical capability to process arrivals by around 30%.
It added the action had been taken "under relevant European regulations". A message on Lisbon airport's website reads: "Due to changes in border control, increased waiting times are expected. Please arrive early at the airport."
Speaking to TTG at WTM London in November, Visit Portugal president Carlos Abade said the Portuguese government had convened a working group to work on EES with a view to "strongly reducing" time taken to transit Portugal's borders.