It is understood the girl was airlifted to hospital but died en route.
Mr Wise said the girl's mother had rushed down to the scene.
He helped comfort one of the girl's four or five mates, who had also been out in the water on paddle boards in the main channel about 100 metres off shore.
The girl, who was on a privately owned paddle board, had been wearing a belt pouch with a lifejacket, he said.
It was unclear whether the yacht was a local vessel, but it had been moored there between two poles for some time, Mr Wise said.
Mr Wise, who has been harbourmaster for two years and deputy harbourmaster for seven years, had been coming to Whangamata for six decades.
"I have never heard of anything like this before. It's an absolute tragedy."
It is not known whether the girl was a local, or was holidaying at Whangamata.
Senior Sergeant Graham Shields said emergency services were called to the wharf off Beach Rd at Whangamata Harbour about 2pm after reports of a paddle boarder trapped under a boat.
"At this stage we can't confirm the exact circumstances but it appears that the boat was moored at the time and a teenage girl on the paddle board was swept underneath by a combination of wind and a strong current," Mr Shields said.
People at the scene rescued the girl and began CPR.
The resuscitation was taken over by medical and ambulance staff when they arrived but the girl could not be revived.
"A lot of people worked really hard to keep her alive and our thoughts are with them and her family," Mr Shields said.
Some of the girl's family had been at the scene and they were being supported by police.
Police were now trying to establish what happened.
"We will work with the Waikato Regional Council harbourmaster to establish exactly what occurred and see if anything can be learned to prevent repeat incidents in the future," Mr Shields said.
The incident was a reminder of how quickly a fun time on the water can go wrong.
"Seventeen agencies, including Police, Surf Life Saving and the Waikato Regional Council, who employ the harbourmasters, have all been working under the umbrella of the Safe Summer Coromandel campaign to prevent deaths on the Coromandel this summer.
Regional council staff in particular have spent long hours on the water over the last few weeks trying to keep people safe.
"At this point the agencies urge people to take the time to identify what tides and currents are doing and never underestimate the power of moving water.
"Also be aware of the limits of your own abilities in the water," he said.
- additional reporting NZME.
