In a statement, the airport said flights had been suspended from shortly after 9pm on Wednesday due to two drones in the vicinity of the airport.
The airport's chief operating officer Chris Woodroofe said that there was still an unauthorised drone over the airport at 8am this morning.
He blasted the "irresponsible" act, telling BBC Radio 4's Today that 10,000 people had been affected by the closure, including 2,000 whose flights had been unable to take off.
He said there were two drones which had been seen flying "over the perimeter fence and into where the runway operates from".
Mr Woodroofe said: "They disappeared and reappeared over the night period from 9pm until 3am, at which point we reopened the runway.
"That lasted 45 minutes before the drones reappeared again and we are currently closed and it is our intention to review the situation when we have daylight at 8am."
r Woodroofe added that the drones had sparked "very significant disruption for passengers" but that police did not want to shoot them down because of the risk from stray bullets.
He told Today: "Last night there were 10,000 people disrupted.
"There were 6,000 people flying in from around the world to Gatwick who were diverted to alternative airports as we closed, there were 2,000 people who didn't take off from their origin airport and there are a further 2,000 people here who couldn't fly to their destination because the airport closed."
He added that 20 police units from two forces were hunting for the pilot, saying: "The police are looking for the operator and that is the way to disable to drone.
"We also have the helicopter up in the air but the police advice us that it would be dangerous to seek to shoot the drone down because of what may happen to the stray bullets."
In the latest statement on the incident, a Gatwick spokeswoman said: "Flights to and from Gatwick Airport remain suspended following reports of drones flying over Gatwick's airfield last night and in the early hours of this morning.
"We are advising passengers scheduled to fly from Gatwick not to travel to the airport without checking the status of their flight with their airline this morning. We apologise for the inconvenience, but the safety of all passengers and staff is our first priority."
By PressÂ Association