Penny said the shooting was related to an earlier police callout at an Onehunga property.
A woman called police to report a family member had been acting erratically. She left the house because she feared for her safety.
Police were sent to the property about 3.10am, but by the time they arrived no people or vehicles were there.
About 20 minutes later, a rural police officer heading home from a shift saw a car pulled over with its hazard lights flashing on State Highway 1 near Topuni.
The car quickly drove off, but the police officer followed until the car stopped again.
As the officer was about to get out of his vehicle, the driver of the car got out and came around to the driver's door of the police car, wielding a machete and threatening the officer.
The officer moved away, called for backup and watched the offender from a safe distance.
The machete wielding man got back into his car and headed south on State Highway 1 towards Puhoi at speeds of up to 150km/h, at times with no lights on.
The Eagle helicopter followed from above while police placed spikes on the road.
The spikes successfully stopped the vehicle near Mahurangi West Rd about 3.50am. But as the first officers got out of the police car, the man, still armed with a machete, approached them again.
Police shot him as he came towards them.
About five police cars and several officers were at the scene when the man was shot. Multiple shots were fired, but Penny could not confirm how many officers had pulled the trigger.
She could not confirm where on his body the man was shot or from what distance.
Penny said officers immediately started first aid and called an ambulance, but the man died at the scene.
The man was from east Auckland, but police would not be able to release his name until he has been formally identified and next of kin informed, she said.
She was not able to confirm whether the dead man was known to police or whether he had been under the influence of drugs.
However, Penny said police believe the man may have been suffering from mental health issues. The death has been referred to the Coroner.
"This is a tragedy," said Penny.
"No police officer throughout the country comes to work and wants this situation to unfold."
The officers involved had been spoken to but hadn't been stood down, she said.
A 27km section of State Highway 1, between Woodcocks Rd and Silverdale, was closed will police gathered evidence. It reopened at 3.55pm.
The shooting was a "rare but significant" event, Penny said.
"It was fast-moving. Every day police staff deal with situations that are complex, dynamic and fast changing. Our staff have to make split second decisions, in situations where there is risk to their lives and members of the public."
Police would also make inquiries into the incident at the Onehunga property to gain a wider picture of what happened.
The Police Association said its thoughts were with the family of the man who had been shot and that the association was there to support the officers involved in the shooting.
The man killed yesterday was the 11th person to be fatally shot by police in New Zealand in the last six years.
Independent Police Conduct Authority chairman Judge Sir David Carruthers last year raised concerns about a spate of shootings in 2016. There were six shootings during the financial year - three fatal and three non-fatal.
"They are, of course, at the highest level of concern for any Police oversight organisation and we are keen to play our part in ensuring that the use of force operates within well understood limits and in the case of ultimate force is always the final tactical option and never the first," he said at the time.
He said the organisation would look into the shootings during 2016 to see if there were any patterns and publically release a report on the findings.
The report had not yet been completed.
Last month, the Police Association said a 2017 survey found one in eight police officers reported being threatened with a firearm at least once in the last year, a 38 per cent increase on the 2015 survey results.
On the front line the figure jumps to 21 per cent threatened at least once in the past year.
