Disgruntled travellers said it took three-and-a-half hours to get through passport control while others complained of a lack of a social distancing and mask wearing.
The delays were so bad many holiday-makers were forced to wait on the tarmac for hours, unable to disembark from planes.
In a tweet the airport said they were working with Border Force to find a solution as quickly as possible. Gatwick, Edinburgh and Manchester airports have also been affected by the issue.
Documentary maker Louis Theroux posted a picture to Twitter showing long queues and described the situation as a “human logjam”.
We’re aware of a systems failure impacting the e-gates, which are staffed & 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.
— Heathrow Airport (@HeathrowAirport) September 24, 2021
An estimated 180 passengers had to wait for an hour onboard a BA flight after it touched down from Nice while queues appeared to go right up to the plane exits inside the airport.
Rubbish from drinks and snacks littered the ground as passengers then had to walk up to 300 metres to join the queue at Terminal 5.
Phil Dean, 52, from Ascot, said: "First of all, we were held on the runway for a while and the gate was not attached so we were held on the plane.
"Passengers are very cross. Even with the e-gates down, people do not understand why there should be such long queues. There are also some people missing connecting flights.
“I don’t know where the pilot is getting his information from because staff at the airport aren’t telling him anything, but he is hoping to know more when they open the doors.
“The planes are full these days and it is a long time for people to be waiting in such conditions.”
Kishore Bala, 24, was travelling with her four-year-old daughter.
She said: “I arrived this morning just before noon and it took me three-and-a-half hours to get through passport control.
Human logjam at Heathrow - apparently all the e gates at all the airports are down? That’s what the man just said. pic.twitter.com/BcJ9So3JVp
— Louis Theroux (@louistheroux) September 24, 2021
“We are travelling with a kid and she had to stand in the queue for hours. We didn’t sleep for the whole night because of our journey.”
“Appalling service. We got through Calgary airport within 10 minutes. You should feel shame.”
Edinburgh airport said Border Force were working to rectify the “IT issue”.
“Passengers will still be able to pass through the Border but this will take a little longer than usual while the issue is resolved. Thanks for your patience,” they said in a statement.
It’s all going swimmingly at Heathrow today. Border Force systems are down? No problem. Bunch everyone up in a queue pic.twitter.com/BHjFG3Km9D
— Matt Ford (@The_Matt_Ford) September 24, 2021
Gatwick airport has managed to prevent long queues so far and said its staff have opened more manual desks to help passengers pass through immigration.
Border Force has over 270 e-gates at 15 air and rail ports around the country “to enable quicker travel into the UK”.
A Home Office spokesperson said: “This afternoon 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 apologise to all passengers for the inconvenience caused.”