"As a precautionary measure, we have stopped departures while we investigate", the statement said.
The runway has now re-opened but numerous passengers are likely to have been caught up in the disruption.
While that would boost punctuality, "flight paths could overfly areas that are not affected by Heathrow arrivals today", the airport said in the study on proposed airspace changes.
Naturally, disgruntled travellers have taken to Twitter to air their views, and at the time of writing it doesn't look like there's much clarity being shed on the situation.
All departures were stopped "as a precaution" shortly after 5pm, leaving passengers stranded on the runway just weeks after a similar debacle caused chaos at Gatwick.
Heathrow Airport is a crossroads for the world, serving 78 million passengers in 2017.
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Another wrote; "Grounded at #Heathrow whilst waiting to fly home to Manchester, first officer says flights suspended whilst police investigate possible #drone activity".
Arriving planes, however, continued to land at Heathrow.
York said he is "absolutely certain that there was a drone flying throughout the period that the airport was closed". At present the law state that if a drone endangers the safety of an aircraft it is a criminal offence and carries a prison sentence of up to five years.
This latest disruption comes after Gatwick Airport was thrown into pre-Christmas chaos last month amid multiple drone sightings.
About 1,000 flights were cancelled there over three days due to the drone sightings.