Airline passengers faced disruption on Wednesday night after an IT glitch resulted in extended queues at immigration desks.
Lengthy queues have already started forming at airport terminals across the country after a fault on UK Border Force computers on Wednesday afternoon.
Extra staff have been drafted in to try and reduce the queues.
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."
Passengers across the country have already reported problems at passport control desks, mostly affecting those trying to enter the country.
The problem is having a particular impact on non-EU airline customers.
A Heathrow spokesman said: "There are some longer queues than normal in the terminals, but we have spoken to border force and they are putting on extra staff.
"Obviously we want to sort the issue out but not risk the integrity of the border controls."
A Birmingham Airport spokesman said: "We are aware (of the glitch) and the impact it is having at the moment.
"It appears to be getting progressively worse but we are hoping it will be sorted out soon."
A Gatwick spokesman added: "We are experiencing similar (problems) to the rest of the airports, and we are working to get people through.
"People should be able to get off the plane, it is those coming through the immigration process which it is frustrating."
The spokesman said there should not be any delays to flights leaving UK airports.
Chris Hyland, a 32-year-old company director from Islington in north London, said international passengers at Gatwick had been told to expect a wait of up to four hours.
He said: "We landed from Geneva at 5.20pm but it took until 6.40pm for us to get through passport control.
"It's an absolute nightmare. We've been told there is an IT failure but that's it.
"You would have thought there would be a back-up plan."
Mr Hyland said non-EU passengers are preparing for a long wait to officially enter the country.
He said: "It is very frustrating. Nobody is really saying anything.
"The international queue is pretty huge, so people have already started sitting down because they know they will be there for a long, long time."
Manchester Airport said some passengers had experienced a slight delay, but that the queues had now gone down.
A spokesman said: "Passengers have been coming through without any significant delays, but we haven't had a large flight in for a bit."
Passengers said they have been told to wait for several hours as staff battle to overcome the problem.
A Glasgow Airport spokesman said it was "largely unaffected" by the glitch.
He added: "There is no issue at the moment here. There will be a flight later from Dubai but we have been largely unaffected so far."