"Pilots flying at the time of the fault would have lost all radar communication," New Zealand Air Line Pilots' Association spokeswoman Lisa Williams was quoted as saying, Stuff.co.nz reported.
"It is an extremely rare event," she said.
Airways Corporation, which manages the radar system, apologised to all passengers who have been affected by this outage.
Flights across the country have gradually resumed after a radar fault, which affected the entire country.
Airways said around 50 airborne flights had been directly affected by the fault.