The airline said the problem has been resolved but services may still be subject to delays.
It led to delays of about two hours for passengers on Monday.
BA hasn’t disclosed what the issue was but media reported a glitch with filing flight plans electronically.
Flight crews apparently had to manually call into the flight operations centre to do so.
“Our teams worked hard to resolve an issue. We’ve apologised to customers for delays to their flights and ensured they were able to reach their destinations as planned,” the airline said earlier.
The outage affected international inbound flights too as well as departures from the three London airports.
Due to the timing of the system outage, it could well lead to a knock-on affect for early Tuesday departures.