BA said in a statement: “We are checking in customers at Heathrow and Gatwick Airports this morning, although it is taking longer than usual.”
Responding to passengers on Twitter, the airline wrote: “We apologise to our customers for the delay and we appreciate their patience as our IT teams work to resolve this issue.”
It added: “Our colleagues are doing everything possible to check in customers for their journey.”
One passenger stranded at Toronto Airport said: “I guess the check in application is down and it’s world wide.”
Flights were disrupted at the airport, in the Royal Docks area of the capital, after activists apparently in support of the Black Lives Matter movement made their way air-side at around 5.40am on Tuesday.
An airport spokesman said: “We’re currently experiencing disruption to all flights due to protesters at the airport. Police are currently on the scene.”