The pilot made it out safely and is in what paramedics described as a "moderate condition". The aircraft involved belongs to Auckland Seaplanes, based at the Sealink Base North Wharf in Freemans Bay.
The company told the Herald they were reviewing the incident and were not prepared to make a statement at this stage.
St John said just before midday that an assessment was being made to see whether the pilot - whose gender and age have not been released - needed to be taken to hospital.
A witness on board a passenger ferry nearby described harrowing scenes when the plane hit the water.
The witness, who only wanted to be known as Rosalyn, said: "It was flying and all we could see was it kind of coming towards the surface of the water. And then when it hit, it nose-dived and it was upside down. Wheels up in the water.''
Rosalyn said despite the crash-landing, the aircraft remained intact.
She said immediately after the crash, their ferry turned back towards the site to help.
"It was quite far away [from us when it crashed]. We turned back around...We didn't know what was going on in the back. But we got really close to help out.''
But she said several nearby boaties immediately turned towards the scene and jumped into the harbour also.
Police said there was one occupant inside the plane and they had made it out of the aircraft safely.
Police said they were notified of the crash, which took place several hundred meters off shore, about 11am.
Witness Murray McLaren on the Pine Harbour ferry said crew members told him the seaplane pilot had escaped.
"From what the crew told me on the ferry the pilot is okay. He got out."
The seaplane had "pitchpoled and it's gone upside down. The nose has dug in and it's flipped right over", McLaren said.
"I don't think it will sink properly because it's on floats but it's not in good shape."
Brett Sharp was driving north over the harbour bridge at about 11.05 this morning when he saw private boat owners "charging" to the crash site to help out.
"I heard about the crash on the radio and looked across and then sure enough there would have been close to a dozen personal boats all trying to help out," he said.
He said it was hard to see but as far he could tell the plane had "flipped up and over".
"It looked like we could make out the seaplane's pontoons in between the boats gathered to help."
