The airline said some flights had been cancelled due to the unspecified technical problems and passengers are being told to check-in online before they travel.
It said in a statement: "We are checking in customers at Heathrow and Gatwick Airports this morning, although it is taking longer than usual. We are sorry for the delay to their journeys."
Flights from airports in the US and Canada have also been affected, while issues were reported in Mexico and the Bahamas, according to CNN
BA told customers on its Twitter feed that it was working had to fix the issue.
The carrier suffered an outage earlier this year which prevented some customers from booking and checking-in for flights while an upgrade to its IT systems in July led to lengthy queues at Heathrow and Gatwick airport.
Meanwhile, travellers leaving from London's City airport have also been hit by delays on Tuesday morning due to protests.
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