A fault in the IT system the UK Border Force uses to scan passports caused hours-long queues at airports and seaports on Wednesday.
The IT problems were "temporary" and all ports are now functioning normally thanks to work carried out overnight by engineers, according to immigration and security minister James Brokenshire.
He said: "We apologise for the delays that some passengers experienced at passport controls yesterday, but security must remain our priority at all times.
"I visited Heathrow early this morning and have asked technical staff to continue to look into the incident to ensure lessons are learnt."
A Home Office spokesperson explained: "Not every port and airport was affected to the same extent. Passport checks were still being carried out, but staff were working on slower systems so that meant delays at passport control for some passengers."
The department did not provide further details about the fault or what caused it.
According to Iain Chidgey, EMEA VP of software company Delphix, software glitches are nearly always a result of insufficient testing.
He said: "The databases used by the UK Border Force are incredibly large and complex which makes testing difficult as the time it takes to make a replication of the databases to test on takes so long that the data itself is often old."
He added: "Companies need to make testing a priority and equip their IT teams with technology and resources that will enable them to test often and on recent data."
The Public Accounts Committee described the Border Force's IT systems as "inadequate" in December last year, warning that its border checks system is "at risk of collapse".
The report also described the Border Force's future development plans as "unrealistic" given the lack of procurement activity for the new technology required.
The government recently confirmed that it has scrapped the troubled e-Borders scheme, originally introduced in 2007 with an aim of ensuring checks on all passengers entering and leaving the UK by 2014.
UK Border Force director Sir Charles Montgomery told MPs in March that he hopes universal exit checks will be in place by 2015 but it is currently unclear what, if anything, will replace the scheme as a whole.
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