The problem affected passport scanners and caused extended delays and queues at immigration desks, with non-EU passengers worst affected.
Huge queues began forming at airports including Heathrow, Birmingham, Manchester and Gatwick.
Some frustrated passengers got into fights.
One passenger at Gatwick, Kay Perry, told Sky News: “We joined the queues at Gatwick’s south terminal which actually extended out of the passport control room, up the stairs and along the corridors.
“We had people merging from the north and south terminal. Nobody really knew where they were meant to join the queues so fights started to break out.”
Extra staff were drafted in to try and reduce the queues and assist passengers.
A government spokesman said: “We are currently experiencing temporary IT problems which may add to the time taken to conduct passport checks.
“We are working to rectify this issue and are providing extra staff to get passengers through the controls as quickly as possible. Our priority remains security of the border.
“We apologise for any additional time this adds to passengers’ journeys.”
For the UK Border Force it is the first major problem they’ve faced since the long queues at the 2012 Olympics.
Image via Getty
