York told BBC Radio 4's Today programme: "Of course, we will have launched our own Sussex Police drones at the time with a view to investigate, with a view to engage, with a view to survey the area looking for the drone, so there could be some level of confusion there."
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Last week, Detective Chief Superintendent Jason Tingley of Sussex Police accepted there may have never been a drone in the air, insisting officers were "working with human beings".
But a Sussex Police spokeswoman told The Telegraph: "Disruption at Gatwick airport was caused categorically by illegal drone activity and not as a result of any use of police drones.
"No police drones were in operation at the start of the incident and were not launched at all unless in response and only when the airport was closed."
Two damaged drones found by police near Gatwick Airport have now also been ruled out of involvement in the incident which disrupted hundreds of flights before Christmas.
Sussex Police's most senior officer told the BBC police have searched 26 potential launch sites for drones near the airport but do not believe they have found the drone thought to have been flown near runways on December 19 and 20.
"I don't think we have found the drone responsible for this at this time," said the Chief Constable.
"I think the fact that we have found two drones so far as a result of this does show the extent of the search that has been carried out. I am led to believe that we are able to rules those drones out of this investigation at this time."
Despite there being no known photographs nor videos of the suspected drone, York remains adamant there was at least one circling Gatwick before Christmas.
He said he was "absolutely certain that there was a drone flying throughout the period that the airport was closed".
York confirmed that military technology was now in place at Gatwick, though he declined to identify the nature of the equipment.
"The systems that are in place today are dramatically different to what was in place a week ago," he told Today.
Asked whether he could rule out a repeat of last week's disruption, York said: "I don't think you can ever rule out anything happening again.
"But what we can say is what is at the heart of this is ensuring it is safe for the aircraft to take off and that's the different position that Gatwick Airport finds itself in today."
Sussex Police have faced calls to hand over the investigation to Scotland Yard, and has been heavily criticised for its handling of the Gatwick incident, in particular the arrest of two innocent West Sussex residents.
York said he was "really sorry" for Paul Gait and Elaine Kirk, who said they felt "violated" after being questioned for 36 hours in custody before being ruled out of involvement in the disruption of Gatwick.
However, he said he was "convinced that the grounds for arrest - the lawful suspicion - in the first instance was well founded".
Gait's boss John Allard told The Telegraph the investigation had been handled "appallingly", and said he tried to contact Sussex Police to tell them they had arrested the wrong man, but was told he could only leave a message and did not get a response.
Describing Sussex Police's approach as a "complete overreaction", he added: "[They] had to seem like they were doing something...they have to find a scapegoat somehow and unfortunately it's somebody who would not harm a fly.
"Paul works as part of three man team who were all on site working on a project in Groombridge, Kent. We could have proven where he was."
