Pictures posted on social media showed frustrated passengers stranded inside planes before take-off – as the UK's second busiest airport was thrown into chaos.
Several jets were forced into holding patterns above the travel hub before being diverted to alternative airports as authorities searched for the rogue aircraft.
Dozens of flights were also forced to change course as far away as Paris, Manchester, Liverpool, Cardiff and Birmingham.
A police helicopter was spotted searching for the drones and their operators, according to reports.
Shocking footage posted online appeared to show one of the drones hovering just yards away from a packed passenger plane.
There was further confusion for passengers this morning after Gatwick Airport announced at 3:30am that runways had reopened.
But it later deleted the tweet and issued a fresh statement confirming the airport remained shut down – after a further drone sighting at 3:45am.
Traveller Richard Asquith told the Evening Standard that his flight from Glasgow circled Gatwick for 20 minutes before being diverted to Stansted – and then to Heathrow.
Passenger Lyndsey Clark said she was on the journey from hell after her Gatwick-bound flight landed at Stansted.
She claimed she was stuck on her Thomas Cook plane on the tarmac for four hours – with a man opening the plane door and another person allegedly saying he was a terrorist.
She posted an image on Twitter appearing to show two transport cops on board her plane.
Twitter account Flight Alerts claimed that at around 9.45pm all inbound planes to the airport were being held and no jets were allowed to depart.
The account tweeted: "Police helicopter is searching the area around London Gatwick Airport.”
Passenger John Belo, who was being held on a plane stranded on the runway, tweeted his frustration at the disruption.
He said: "Still waiting for my flight to depart from @Gatwick_Airport – waiting for security checks on runway due to drone reports…"
The airport said it was investigating and apologised to passengers for the inconvenience – stressing that safety was "our foremost priority".
An earlier statement read: "Following reports of two drones flying over the Gatwick Airfield, we have had to suspend flights while this is investigated.
"We apologise to any affected passengers for this inconvenience but the safety is our foremost priority."
British Airways apologised to its customers after confirming that its flights were suspended.
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