Police suspended operations for the rest of the shift as a precautionary measure. The chopper was inspected and crew were interviewed by detectives.
"Our Police helicopter is responsible for saving lives and keeping our community safe," said Wilson.
"The actions of these people in flying a drone dangerously close to the Eagle helicopter is totally irresponsible and Police will investigate thoroughly.
"This could easily have ended in a tragedy and it is a worrying reminder of the dangers of flying drones near other aircraft."
Wilson said it is believed there were also two other unauthorised drones in the immediate vicinity and police are now working with the Civil Aviation Authority.
Normal operations have resumed this morning.
Wilson said the incident marks what was otherwise a mostly well-behaved New Year's Eve across the country.