British Airways has cancelled all short-haul flights from Heathrow until midday on Saturday.
The airline apologised and warned of further disruption due to ongoing technical issues.
Long-haul services at the airport and all flights at both Gatwick and London City are expected to go ahead but there may be delays, British Airways said.
Heathrow said it was supporting the airline in tackling the IT problems and requested passengers to check the status of their flight before travelling to the airport.
BA’s website and app were unavailable for hours on Friday evening, preventing customers from checking in online or booking flights.
It is the airline’s second outage in 10 days and follows disruption caused by Storm Eunice which delayed luggage handling.
In a statement, British Airways said: “We are extremely sorry that due to the continuing technical issues we are facing we have regrettably had to cancel all short-haul flights from Heathrow today until midday. Customers due to travel later today should check their flight status on ba.com before coming to the airport as we anticipate further disruption during the day.
“Our long-haul services at Heathrow and all flights at Gatwick and London City Airport are due to operate as planned, but customers may experience some delays. Our website ba.com is working and customers can check-in online and at the airport.
“We are offering customers on cancelled services options including a full refund and all customers booked to travel on short-haul services from Heathrow today can opt to rebook to a later date for free if they choose. We will be contacting customers proactively.
“Our teams have been working hard through the night and will continue to do so to resolve the issue as soon as possible. We advise our customers due to travel today to check ba.com for the latest flight information before coming to the airport.
“We know we have let our customers down and we will do everything we can to make this up to them – but for now our focus is on getting as many customers and flights away as we can.”