Passengers are seen in front of the check-in counters in Terminal 1 at Berlin Brandenburg Airport in Sch’nefeld,Germany (Picture: AP)

The cause behind the disruption of operations at Europe’s largest airports has finally been confirmed as a cyber attack.

Hundreds of flights were delayed – and some cancelled – across Heathrow Airport,Brussels Airport and Berlin Brandenburg Airport – on Saturday amid a cyber-attack affecting an electronic check-in and baggage system.

Authorities at Brussels Airport said a cyber attack on Friday evening meant that travellers were being checked in and boarded manually.

Other airports had not commented on the exact reason behind the delays.

RTX,which owns software provider Collins Aerospace,said it was ‘aware of a cyber-related disruption’ to its system in ‘select airports’ and that it was working to resolve the issue as quickly as possible.

The European Union’s cyber security agency,ENISA,has now said that the problems with automatic check-in systems were caused by a cyber attack.

A statement confirmed that law enforcement is involved to investigate.

Passengers are still suffering the repercussions of the incident,while work is ongoing to ‘resolve and recover’ from the ‘outage’ in the system.

One traveller described the boarding process as akin to the early decades of commercial air travel,with handwritten boarding passes.

Brussels Airport was using iPads and laptops to check people in online.

Of roughly 550 departing and arriving flights,60 had to be cancelled on Monday,it said.

Collins Aerospace said today that it was working with the affected airports,including Brussels and Heathrow,Europe’s busiest airport,and was in the final stages of completing updates to help restore full functionality.

Berlin airport,which was facing higher passenger numbers than usual on Monday due to the Berlin Marathon,still did not have its check-in systems restored and reported delays of over an hour for departures.

Delays at Europe's busiest airports