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Reports of loud ''bangs'' followed by houses shaking began about 5pm, in the Hibiscus Coast area.
Inspector Tony Edwards of police northern communications said police received reports of the bangs from the Herald Island - Greenhithe area about the same time.
More reports came in a while later from the Ranui - Scenic Drive area in West Auckland.
A Fire Service worker came in to work later and confirmed they had heard the noises in the Red Beach area, which is on the Hibiscus Coast.
Edwards said people had variously described the noises as sounding like gun-shots and loud explosions.
Police had checked with the Air Force, which has a base in Whenuapai, but turned out not to be not responsible, and neither was Paremoremo prison.
Lines companies had not reported any electrical disturbances and Geonet is not showing any tectonic activity in the Auckland area.
Arkles Bay resident Will Trayes said he heard the noises about 4pm.
His house shook with a "sudden, quick vibration" for two or three seconds and he heard a slight rumble similar to thunder.
Six or seven minutes later it happened again and then again six or seven minutes after that.
His sister said she thought it was a truck going past the house, he said.
''I wasn't worried, I was just wondering if there was going to be a bigger shake."
A local Facebook page was inundated with 450 comments after Kelly de Rooy posted: "Holy hell, was that an earthquake I just felt in Stanmore Bay? My entire house just shook".
Sally Louise Dodsworth wrote: ''3 big shakes here in Stillwater'' while Deborah Johnston said: ''We heard real weird noise too and the cupboards were vibrating in Red Beach.''
Kathryn Wales wrote: ''Can anyone see Rangitoto???? That's not blowing up is it???''
Astronomer Alan Gilmore, at Tekapo's Mt John Observatory, discounted the theory that it could have been a meteor creating a sonic boom.
Gilmore was interested at first, saying it was possible and there had been other meteor-caused booms in New Zealand in the past.
However, his enthusiasm dimmed when told there were reports of three bangs five minutes apart.
The chance that three meteors would all strike in the same place separated by a regular interval was very, very low, he said.
"I think you'll have to look for a terrestrial explanation," he said.
The noises remain a mystery.
I have just listened to an interview on Radio New Zealand with the NZ Airforce chief. Yesterday they denied responsibility and the chief said he was unaware of this denial. Today they are claiming they have been testing bombs dropped from the Airforce Orion aircraft. They did not expect the sound to travel so far to where the noises were heard but due to conditions; wind direction and cloud cover the sound travelled. They are continuing testing tomorrow and next week. This is occurs "about anually" he said.