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The near-miss happened on Sunday when the Auckland Westpac Rescue Helicopter lifted off from Mechanics Bay at 8pm on the urgent mission.
Pilot James Tayler said the chopper had climbed to 400 metres and was flying at 230kmh when the crew saw a drone pass down its right hand side about 3-4m away.
"If we had hit the drone, it would have definitely done serious damage to the helicopter, possibly catastrophic if it had hit a rotor blade or other critical component," he said.
"If it had hit the windscreen, it would almost certainly have broken it and injured the crew."
The accident scene the helicopter was attending was the result of a two-car crash on State Highway 1, north of Moerewa, between Hautapu Rd and Nisbet St, about 7.30pm.
Following the crash, a young boy was flown to Starship Hospital with critical head injuries, and emergency services also assisted a woman in a critical condition.
One other person received serious injuries, while two more had moderate injuries. All were taken to Bay of Islands Hospital for treatment.