Chaos sparked at the UK's biggest airport on at 5.05pm following reports of a drone sighting.
"As a precautionary measure, we have stopped departures while we investigate".
"It is crucial that our plans maximise the benefits of expansion across the country, including for the communities closest to us", said Emma Gilthorpe, Heathrow's Executive Director for Expansion. "We apologies to passengers for any inconvenience this may cause".
Heathrow staff are working with the Metropolitan Police and all flights have been grounded "as a precaution", an airport spokesperson said.
Transport Secretary Chris Grayling said the military was "preparing to deploy the equipment used at Gatwick at Heathrow quickly should it prove necessary".
Throughout the emergency, the south runway remained open, allowing planes to land.
John Stewart, of the Heathrow noise reduction campaigning group Hacan, said: "Although a third runway will clearly bring many losers, one long-lasting impact of these proposed changes is that a break from aircraft noise would be guaranteed to many more people than who now enjoy it, as Heathrow would make the biggest changes to its flight paths since opening in 1946".
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ITV reporter Sarah Rodgers was among those now grounded at Heathrow. "Like WTAF?!", one wrote. "Apparently we can't take off due to #drone sighting!"
In a separate consultation a year ago, most respondents rejected the idea of concentrating more planes over the same area and asked the airport to vary flight paths, which is likely to affect thousands more homes.
David Zuelke wrote: 'Sitting on plane on runway at Heathrow Airport. "Would seem that I should expect 2-3 days wait?"
York said he is "absolutely certain that there was a drone flying throughout the period that the airport was closed".
BBC producer Kathy Long, speaking from a plane waiting to depart at Heathrow, confirmed passengers were told they won't be departing in the near future.
More than 140,000 passengers at Gatwick were affected during 36 hours of chaos between 19 and 21 December.
A senior detective also said at one point it was possible drones hadn't flown over the airport, sowing confusion, but police later insisted the drone sightings were authentic.