The agency that monitors the country's airspace says it is "highly unlikely" yesterday's radar system failure was the result of hacking.
The Transport Accident Investigation Commission has opened an inquiry and Airways New Zealand is undertaking an internal investigation.
Airways chief operating operator Pauline Lamb said hacking was among the options immediately considered after yesterday's radar failure, but has largely been ruled out.
"It certainly was one area that we went into immediately because you've got to be open to every eventuality," she said.
"But it's highly, highly unlikely that this event was caused by any such penetration."
She said accessing the system required six levels of authentication and there was no evidence to suggest the network had been hacked.
Ms Lamb said the internal investigation was focusing on three errors that potentially triggered the system breakdown, though she would not say what the errors were.
She said the fault was the result of equipment failure that stopped data being distributed to air traffic controllers.
Fifty planes were in the air when the network failed and controllers had to guide them down using reports from pilots by radio.
Four minute outage
Airways noticed the fault about 2.40pm yesterday and grounded all commercial flights around the country. More than 200 flights were affected. The radar went back into full service about 4.30pm, but flight delays continued for the rest of the day.
Ms Lamb told Morning Report that the system itself was down for only four minutes, but staff had to check it was working properly before restarting flights.
Pilots' association spokesperson Lisa Williams said the breakdown was potentially serious.
"This is when the controller really relies on the pilot's position reports to provide separation between aircraft, because obviously visually they've got to see what's going on."
Pilots and air traffic controllers deserved praise for the way they handled a stressful situation, said Ms Williams. "It was certainly a potentially serious situation."
Ms Lamb said fallback procedures were in place that "enable us to handle the traffic safely in these situations."
"This particular situation was indeed very undesirable ... but because we have procedures in place which the pilots know about, which the controllers know about, we're able to handle the situation safely."
The fault affected only domestic airspace. "Our Oceanic system which looks after the Pacific and the Tasman was not affected in this case."
A team of three Transport Accident Investigation Commission investigators has started gathering evidence. The commission said a typical investigation may take up to 18 months but safety recommendations can be issued at any time.