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Heathrow drafted in extra staff after a reported cyber attack hit electronic check-in and baggage systems over the weekend.
The London hub warned of possible delays due to a "technical issue" affecting software provided by Collins Aerospace to several airlines.
Brussels airport said that a cyber-attack on Friday night meant that passengers were being checked in and boarded manually, while Berlin’s Brandenburg airport also reported longer waiting times due to the issue.
The airport continued to warn that flight cancellations and delays today (Monday).
A statement from Brussels airport said: “Following a cyber attack on the American company Collins Aerospace, the external provider of check-in and boarding systems, there are disruptions to check-in operations at several European airports, including Brussels airport.
“The service provider is actively working on the issue and trying to resolve the problem as quickly as possible. At the moment it is still unclear when the issue will be resolved.”
Other airports affected included Frankfurt, Paris Charles de Gaulle and Munich.
RTX, which owns Collins Aerospace, said that it was "aware of a cyber-related disruption" affecting its system in "select airports" and was working to resolve the issue as quickly as possible.
It said the attack hit its Muse [multi-user system environment] software, which allows different airlines to use the same check-in desks and boarding gates at an airport, rather than requiring their own.
A National Cyber Security Centre spokesperson said: “We are working with Collins Aerospace and affected UK airports, alongside Department for Transport and law enforcement colleagues, to fully understand the impact of an incident.”
A Heathrow spokesperson said on Saturday: “Collins Aerospace, who provide check-in and boarding systems for several airlines across multiple airports globally is experiencing a technical issue, which may cause delays for departing passengers.
“While they are working to resolve the problem quickly, we advise passengers to check their flight status with their airline before travelling to the airport and arrive no earlier than three hours before a long-haul flight or two hours for a domestic flight.
“Additional colleagues are available in check-in areas to assist and minimise disruption. We apologise for any inconvenience.”
Aviation analytics firm Cirium estimated that 14 out of 651 Heathrow flights were cancelled on Saturday and seven out of 673 on Sunday.
However, as many as 82% of flights on Saturday and 51% on Sunday faced delays to within 15 minutes of their scheduled departure time.
Lisa Webb, Which? consumer law expert, said: "These delays and disruption will be incredibly disappointing for thousands of travellers hoping to fly from Heathrow. Although this issue is not the fault of the airlines, they still have a legal duty of care to customers.
“Airlines will understandably be overwhelmed so passengers may have to be patient but they should not hesitate to get in touch and ask for the help they’re entitled to."