Thousands of airline passengers faced extreme delays yesterday (Wednesday), with queues of passengers extending into airport corridors.
The government has apologised for the chaos and has now said the IT problem has been fixed - but it declined to specify how many airports are still affected by the problem.
Travellers arriving into the UK last night were told to expect slow-moving queues lasting for up to four hours as staff battled to resolve the issue.
Immigration and security minister James Brokenshire said this morning: "Our engineers have been working through the night to fix the temporary IT problems that regrettably led to longer queues for some passengers at passport controls yesterday.
"The current situation is much improved and we are doing our best to keep waiting times to a minimum during this morning's busy period.
"We apologise for any delays but security must remain our priority at all times."
A Home Office spokesman refused to provide "a running commentary" on the situation. Source: PA.
But they said Mr Brokenshire had been kept updated on the situation through the night and would be at Heathrow this morning with the director general of Border Force to personally oversee the ongoing work to resolve the situation.
Gatwick Airport said an IT glitch affecting the Border Force computer system has been resolved.
The technical problem affected immigration desks at airports and ports nationwide, resulting in lengthy queues for passengers.
Gatwick Airport tweeted: "Yesterday's difficulties with (UK Home Office) IT systems have now been resolved."
A Heathrow Airport spokesman would not confirm if the problem was still affecting its computers but said passengers "were clearing immigration in good time".
He added: "There are no problems affecting Heathrow at the moment."
Extra staff had been drafted in to try and reduce the queues yesterday. Passengers were affected when trying to enter the country, with a particular impact on non-EU airline customers.
A Government spokesman yesterday apologised for the problems. He said: "Our priority remains security of the border."
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 last night.
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."
Hugh Boyes from the Institution of Engineering and Technology said: "This incident highlights the needs for the design and implementation of resilient systems, where the impact of failure on the end user is taken into account. Given our increasing dependence on computer systems, failure to delivery trustworthy systems that support key public services can have an impact on the economy and national reputation."
Passengers fake disabilities to jump airport queues
Drug suspects waved through UK airport security
The ten worst airports in the world