Heathrow, Manchester and Edinburgh airports all reported problems with e-gates.
The gates allow travellers with biometric passports to pass through border control without a manual inspection.
Edinburgh Airport said: "The UK Border Force (UKBF) IT issue is nationwide and UKBF teams are working to resolve this.
"All available UKBF staff are in the arrivals hall to carry out necessary checks and allow passengers to pass through the border as quickly as possible. Thank you for your patience."
Heathrow Airport also added: "We're aware of a systems failure impacting the e-gates, which are staffed and operated by Border Force.
"This issue is impacting a number of ports of entry and is not an isolated issue at Heathrow. Our teams are working with Border Force to find a solution as quickly as possible."