Airline passengers reported delays of up to four hours as airports across the UK were hit by a second e-gate technical fault within two weeks.
Travellers arriving at Heathrow were forced to either wait in long queues in terminals or remain on aircraft.
E-gates, managed by UK Border Force, allow travellers with biometric passports to pass through border control without a manual inspection.
A systems failure caused e-gates to stop working for several hours on September 24, so passengers had to wait to have their travel documents inspected by staff.
The Home Office said it first received a report about the latest “technical issue” at around 7.30am on Wednesday, and the problem was resolved 90 minutes later.
Passengers arriving at Heathrow on Wednesday morning described the queues as a “total disgrace”.
Christian Jones said he was queuing for around an hour on his way back from a trip to Finland.
“The queues were snaking out of the arrivals hall all the way down the corridor and into the connecting flights corridor… I queued for one hour but others, I believe, queued for about four hours,” the 41-year-old from Cambridge told the PA news agency.
Vibhaker, who did not wish to share her surname, was waiting at arrivals in the airport for her niece, who was travelling to the UK to start a masters course in sports medicine.
“The whole area was (a) total shambles heavily crowded with no possibility of social distancing – she got out after three hours… (a) total disgrace,” the 73-year-old told PA.
George Zarkadakis, an artificial intelligence engineer from London, wrote on Twitter: “System for scanning passports is down (again). Expected time of waiting for arriving passengers: 2-4 hours.
“I think I’ll stay home next time… and stick to Zoom calls.”
Another passenger, Thomas de Lucy, tweeted: “Not only are we waiting for two hours at passport control but Heathrow staff are all incredibly rude, shouting at people and ignoring others.
“Maybe a supervisor should be on hand to control staff behaviour.”
A Heathrow spokeswoman said: “Earlier today a systems failure impacted the e-gates, which are staffed and operated by Border Force.
“This issue, which impacted a number of ports of entry, has since been resolved and the e-gates at Heathrow are back up and running again.
“Our teams remain on hand and are working with Border Force to monitor the situation, and to get passengers on their way as quickly as possible.”
A Home Office spokeswoman said: “This morning a technical issue affected e-gates at a number of ports. The issue was quickly identified and has now been resolved.
“We have been working hard to minimise disruption and continue to monitor the situation closely.
“We apologise to all passengers for the inconvenience caused.”