Passengers were forced to wait nearly two hours to get through passport controls from European countries into the UK.
Travellers between Schengen area countries and Britain had to go through stricter security checks over fear terrorists behind the Paris and Brussels attacks used EU passports to travel around the free movement block.
Yesterday Heathrow also saw delays as “total chaos” erupted when the check-in system crashed.
Simon Fletcher, 39, of Forest Hill, south London, who flew back from Paris Orly on business today, was delayed for nearly two hours before he could board the flight.
He said: ‘Our flight was delayed for about an hour and a half, otherwise we would have missed it.
‘We were waiting for nearly two hours to go through passport checks.
‘Normally going through passport controls in Europe is really quick and straightforward, but today the guy on the desk was looking at his computer for about ten minutes.
‘I’ve never seen that before.
‘There were no extra staff on, they knew it was going to be busy with these new checks in place, but no measures were taken to help.’
Phil Davis, who flew back from Frankfurt after a delay of nearly an hour and a half, said the airport only had one security lane open when a number of international flights were leaving around the same time.
He said: ‘There was like 150 people or more in the security lane but only one line open.
‘There was a load of international flights departing around the same time but there was only one lane open. It was awful.
‘I don’t know if it was anything to do with extra security checks or just incompetence on the part of the airport staff.’
Sally Mearse, from Richmond, west London, who was flying to Tel Aviv, was worried she might be delayed by the airport’s computer failure.
The 40-year-old said: ‘I heard there were a lot of queues earlier and I was regally worried.
‘But when I got here it seemed to be fine, just like a normal day.
‘I think they must have sorted it out pretty quickly given that it has happened before.’
Airports in Spain and France seemed to be worst affected, but holidaymakers feared other Schengen counties such as Germany may also introduce the tight controls.
A flight from Munich to Heathrow was also delayed by 45 minutes.
Michael Stenson, 51, of Basingstoke, Hampshire, was flying to Dusseldorf, said: “It doesn’t seem to be affected yet, Germany seems OK.
‘But I’m going to leave an extra hour when I come back because you can never be too sure.
‘It’s strange that they’ve decided to do this now, the Paris and Brussels attacks were two years ago and this has started as Brexit negations have began.’