The spokesman said a flight safety event report would be raised with NZ CAA.
The drone was above Browns Bay, a suburb on Auckland's North Shore.
Operations to and from the air base were suspended for around 30 minutes following the scare.
The incident comes just days after a drone sighting in the Auckland Airport airspace.
Seven flights had their landings delayed after a drone was sighted in the Auckland Airport airspace last Tuesday.
The Civil Aviation Authority of New Zealand (CAA) says a drone was spotted by two pilots on approach to Auckland airport at 2.46pm and was flying at an altitude of around 1200 feet.
It was three nautical miles from runway 05 in the direction of Manukau.
CAA deputy director of general aviation Steve Moore said he was "hopping mad" over the incident.
"Pilots and their passengers should be able to take off and land at our airports without the added risk of a drone coming into contact with their aircraft," he said.
"The idiots who are doing this are putting people's lives at risk and need to be identified before something catastrophic happens.
"The safety of the travelling public cannot be compromised by thoughtless fools flying drones illegally in the airport zones."
Last month Air New Zealand called for tighter regulations regarding drone use after two near misses with drones.
On one occasion a drone came within metres of a flight descending into Auckland Airport from Tokyo, putting the safety of 278 passengers and crew at risk.
The airline said the drone passed so close that the crew worried it had been sucked into an engine, although a later inspection showed that had not happened.
Under current regulations, drone operators who breach aviation rules can be fined up to $5000.
