Around 100 EasyJet customers were abandoned in the Italian city while waiting to board their plane back to Manchester.
The delays were caused by the EU’s new Entry/Exit System (EES) which meant passengers could not be processed in time to board their plane, despite many arriving at the airport three hours early.
The EES system requires people to have their photo taken and fingerprints registered, adding several minutes per passenger.
A blame game has begun between EasyJet and the airport. The airline said the situation was ‘outside of our control’ and added they delayed the plane by 52 minutes in an effort to make as much time as possible for passengers to be processed.
However, the plane was forced to take off because the crew reached the limit of their safety regulated operating hours.
One couple who took their son for an Easter holiday had to wait an hour at passport control when they arrived. On their return they reached the terminal nearly three hours early but still weren’t able to board in time.
Max Hume, 56, his wife Lynsey, 46, and their 13-year-old son Archie were told they would have to pay £330 to be rebooked on the next available flight, five days later. So they spent over £1,600 for a connecting flight via Luxembourg.
Mr Hume said he felt “gutted, upset, let down, absolutely shattered and poorer – much poorer”.
Of the 156 passengers due to board, only 34 managed to get on the plane.
Bizarrely, passengers booked on other ‘non-Schengen’ flights, two on British Airways to Heathrow and an easyJet flight to Gatwick, were allowed through.
Mr Hume added: “People were arriving late for those London flights and they were just letting them through while holding us back.”
“There were two officers and one biometric machine. We had to do face scan, passport scan, and fingerprints. Every single person. But there were about 16 machines that could have been used automatically, and they didn’t open them. So everything was going at a snail’s pace.”
The flight eventually departed but only after offloading all the baggage belonging to more than 100 missing passengers who had not been processed in time.
Read more: Trump ‘doesn’t care’ if Iran returns to peace talks
A spokesperson for easyJet said: “We are aware that some passengers departing from Milan Linate today experienced longer than usual waiting times at passport control and we advised customers due to fly to allow additional time to make their way through the airport.
“We have been doing all possible to minimise the impact of the airport queues, holding flights to allow customers extra time and providing free flight transfers for any customers who may have missed their flight including EJU5420 to Manchester.
“We continue to urge border authorities to ensure they make full and effective use of the permitted flexibilities for as long as needed while EES is implemented, to avoid these unacceptable border delays for our customers.
“While this is outside of our control, we are sorry for any inconvenience caused.”
On Friday, the first day of full EES, the Brussels-based trade association Airlines for Europe demanded “border control authorities must be allowed to fully suspend the EES when waiting times become excessive”.