Mr Wise said the girl's friends managed to get her back on her paddle board and a passing boat helped bring her to shore.
The girl who was riding a privately-owned paddle board had been wearing a belt pouch with a lifejacket, he said
Mr Wise said the yacht was moored between two poles, and it was unclear whether it was a local vessel but it had been moored there for some time.
The girl's mother rushed down to scene, he said.
Mr Wise said he had been harbour master for two years and deputy harbour master for seven years and had been coming to Whangamata for 60 years.
"I have never heard of anything like this before. It's an absolute tragedy."
It is not known whether the deceased is a local, or was holidaying at Whangamata
Waikato Police are working with the local district council to establish the circumstances surrounding the incident.
Area Response Manager for the Thames Coromandel, Senior Sergeant Graham Shields said emergency services were called to the wharf off Beach Rd 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.
"People at the scene rescued her and commenced CPR which was continued by arriving medical and ambulance staff. Sadly these efforts were not successful in reviving her.
"A lot of people worked really hard to keep her alive and our thoughts are with them and her family."
Mr Shields said the priorities for police at present were establishing what had happened and ensuring the victim's family, some of whom who were at the scene, got the support they needed.
"We will work with the Waikato Regional Council Harbour Master to establish exactly what occurred and see if anything can be learned to prevent repeat incidents in the future".
Mr Shields said today's 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 Harbour Master's, 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."