The issue is affecting people arriving in the UK, with queues expected to build quickly.
Passengers flying into the UK are facing delays at passport controls as e-gates across the country are not working.
The issue at airports, including Heathrow, Manchester and Gatwick, began on Friday night.
The Home Office said it was working with airlines and port operators to minimise disruption from the “nationwide border system issue.”
A union warned queues would build quickly.
All airports across the country using the gates are affected, meaning people flying in are having to get their passports checked manually.
It is unclear what the issue is with the border system, with a Home Office spokesman saying it was “too sensitive to say”.
However while it is technically affecting anywhere where people are checked coming into the UK, the impact is mainly being felt at larger airports with e-gates.
This weekend was already expected to be busy for travellers, with the bank holiday coinciding with the half-term break for many families.
Separately travellers leaving the UK from the Port of Dover also faced issues after the French passport system failed earlier on Saturday.
The IT issue has now been fixed, but cars and coaches are waiting for about an hour, with about 400 lorries queuing to make the crossing on what is a busy bank holiday weekend.
Airports around the UK issued statements warning passengers of delays but said they were working with the UK Border Force to minimise disruption.
A Gatwick Airport spokesperson said queues were “manageable” so far – although they were expecting 800 incoming flights on Saturday. It confirmed the issue first started between 19:00 and 20:00 BST on Friday.
The e-gate system speeds up passport control by allowing some passengers to scan their own passports. It uses facial recognition to verify identity and captures the traveller’s image.
One passenger arriving at Gatwick said the situation was an “utter joke”.
Lucy Morton, from the Immigration Services Union, told the BBC that between 60-80% of incoming passengers usually use e-gates, depending on the airport and with them being unavailable queues were likely to build “very quickly”.
“There’s no impact on national security,” she said, explaining that all arrivals will still be fully checked through manned officer desks.
E-gates can be used by British citizens aged over 12 and those from the EU, as well as people from countries including Australia, Canada, the US, Japan and New Zealand.
But all entry points retain manned security desks for other passengers and those unable to use e-gates.
A Home Office spokesperson said they were aware of a “nationwide border system issue affecting arrivals into the UK”.
“We are working to resolve the issue as soon as possible and are liaising with port operators and airlines to minimise disruption for travellers,” they said.
On Thursday and Friday British Airways was also hit by IT issues, affecting more than 20,000 passengers at Heathrow.
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