Heathrow was among several European airports hit by delays on Saturday after a cyber-attack affecting an electronic check-in and baggage system.
The airport said a number of flights were delayed as a technical issue impacted software provided to several airlines.
Brussels Airport said a cyber-attack on Friday night meant passengers were being checked in and boarded manually, and Berlin's Brandenburg Airport reported longer waiting times due to the problem.
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 company added: The impact is limited to electronic customer check-in and baggage drop and can be mitigated with manual check-in operations. It said its Muse software - which allows different airlines to use the same check-in desks and boarding gates at an airport, rather than requiring their own - had been affected.
The BBC understands that British Airways is operating as normal using a back-up system, but that most other airlines operating from Heathrow have been affected.
Shortly before midnight on Saturday, Heathrow said it was continuing to resolve and recover from the outage. It apologised to those who had faced delays but stressed that the vast majority of flights have continued to operate.
A National Cyber Security Centre spokesperson said it was working with Collins Aerospace, affected UK airports, the Department for Transport and law enforcement to fully understand the impact of the incident.
The European Commission, which plays a role in managing airspace across Europe, said it was closely monitoring the cyber-attack and there was no indication it had been widespread or severe.
A spokesperson added that it was working with airlines and airports to restore operations and support passengers.
Hundreds of flights have been delayed throughout Saturday, according to flight tracker FlightAware. Dublin Airport said it and Cork Airport had experienced a minor impact from the cyber-attack.
Lucy Spencer said she had been queuing to check in for a Malaysia Airlines flight for more than two hours, and that staff were manually tagging luggage and checking passengers in over the phone.
Another passenger, Monazza Aslam, said she had been sitting on the tarmac for over an hour with no idea when we will fly and had already missed her onward connection at Doha.
Johnny Lal, due to fly to Bombay for his mother-in-law's funeral, said he and his family would miss their flight as they were unable to access necessary mobility aids.
Transport Secretary Heidi Alexander said she was aware of the incident and was getting regular updates and monitoring the situation.
Travel journalist Simon Calder noted that minor disruptions can escalate quickly in interconnected air travel.
While there are unfounded accusations that this cyber-attack was executed by Kremlin-sponsored hackers, it is noted that many large cyber incidents are perpetrated by criminal gangs driven by financial gain.
Collins Aerospace has yet to comment publicly about the nature or origin of the hack, but many hacking operations are often traced back to groups in Russia.
