Dramatic new video footage shows a catamaran being picked up and tossed over a pier on in the storm on Monday night.
Auckland Council released the footage to RNZ from CCTV cameras on Westhaven Marina on 12 August.
Shipping containers were also blown over, one into the harbour and another onto a car - trapping a person inside.
Described by witnesses as a tornado, almost 50 boats were damaged or broke their mooring in the short but ferocious weather event.
The manager of Westhaven Marina, Kevin Lidgard, was astounded by the video showing the squall hitting the harbour.
"It's just defies belief how it picked up a huge catamaran and just threw it over the pier like a little block of cork."
An overturned catamaran at Westhaven Marina on Tuesday after an overnight storm hit downtown Auckland. Photo: RNZ / Liu Chen
Mr Lidgard said many people were astounded by the amount of damage caused in such a short time.
The Great Barrier Island car ferry also broke off its mooring line and at least two yachts sank in their berths.
Police coastal master John Burridge said he was helping people injured by flying furniture at a restaurant, when he looked up to see the looming ferry.
It was about 50 metres from Captain Cook wharf when he and colleague Kevin Stone attached a tow-line from their rigid inflatable boat (RIB) and pulled it slowly into the middle of the harbour.
"It was a very surreal moment, I was standing on the wharf initially when I saw it, and moving quite quickly with the wind down the harbour," he said.
"And when our RIB turned up and we got on board , there was only two of us on our 12-metre RIB. It's got twin 225 outboard [motors] on the back. And it was a bit of a David and Goliath moment.
"I must admit, when we got alongside it, it's rather large and it's rather heavy and it was blowing a lot. We were just like, oh well I hope we can do this and we managed to stop it so that was great.
"We were really worried that if it had hit the wharf, a) it would have damaged the wharf, damaged the ferry, but it also could have spilled diesel and oils, could have ruptured tanks and put more fuel into the harbour, so we were trying to stop any environmental hazard."
He and his colleagues held the boat for 35 minutes until Coastguard volunteers and tugs from the Ports of Auckland arrived to help guide it back to the ferry terminal.