BA said there was no evidence the problem had been caused by a cyber attack.
British Airways (ICAG.L) resumed some flights from Britain's two biggest airports on Sunday after a global computer system failure created chaos, but hundreds of passengers were still waiting for hours at London Heathrow.
The airline told travellers to check the status of their flights before coming to the airports, and Heathrow said it expected more disruption on Sunday.
Flights from other airlines are running in and out of Heathrow and Gatwick as normal for the time being, so if you're taking off for the bank holiday weekend or half term then your best bet is to check for updates straight from the company you've booked with.
When asked about the disruption at Heathrow, a BA spokeswoman said: "We appreciate that this is a very trying and distressing experience for customers and we are doing everything we possibly can to get them away on their flights as soon as we can".
The airline said earlier on Sunday it was hoping to operate a "near-normal schedule" and apologised for the disruption.
"We would like to say again how extremely sorry we are for the inconvenience this is causing during this busy holiday period", BA said on its website on Sunday.
Air industry consultant John Strickland said: "There's a massive knock-on effect".
On Saturday, passengers at Heathrow and Gatwick faced long lines at check-in counters and the failure of both the airline's website and its mobile app. BA said the crash also affected its call centers.
"Customers and - from the airline's point of view - manpower, dealing with the backlog of aircraft out of position, parking spaces for the aircraft".
"We rebooked for Venice for tonight, which they also have canceled now", she told Sky News.
A spokeswoman for BA could not immediately detail the exact number of flights cancelled on Saturday.
The airline has suffered other IT glitches recently, leading to severe delays for passengers in July and September past year.
BA had issues with its online check-in systems in September and July a year ago, causing severe delays for passengers. He and other passengers arrived, but their luggage did not.
A spokesman said: "Our focus is on updating customers and doing what we can to get them to their destinations as quickly as possible".
Heathrow said the IT problem had caused "some delays for passengers" and it was working with BA to resolve it.