EasyJet and Ryanair, which do not operate out of Heathrow but are among Europe’s biggest airlines, said they were operating as normal.
Brussels Airport said there would be a “large impact on the flight schedule”, including cancellations and delays.
Europe’s combined aviation safety organisation, Eurocontrol, said airline operators had been asked to cancel half their flight schedules to and from the airport between 04:00 GMT on Saturday and 02:00 on Monday due to the disruption.
In a separate incident, Dublin’s Airport 2 terminal has reopened following a security alert. Suspicious luggage was flagged to Gardaí (Irish police) on Saturday, who evacuated the terminal as a “precautionary measure”.
Travel journalist Simon Calder said that “any disruption is potentially serious” at Heathrow, given it is Europe’s busiest airport, and that “departure control is a really complex business”.
He told the BBC: “These things are all interconnected, so a little bit of a problem in Brussels, in Berlin… people start missing connections, planes and passengers and pilots are not where they are meant to be, and things can get quite a lot worse before they get better.”
It was only last July that a global IT crash due to a faulty software update from cybersecurity firm Crowdstrike caused disruption to aviation, grounding flights across the US.
Analysts said at the time that the incident highlighted how the industry could be vulnerable to issues with digital systems.