A police officer at the scene told the Otago Daily Times the missing man was a father.
A Glenorchy resident told the ODT she understood a father and son got into trouble in the water.
A St John spokeswoman said an ambulance, a first response unit and a helicopter were sent to the scene.
One patient with minor injuries was taken to Lakes District Hospital by road.
A second helicopter was stood down before it arrived at the scene, the spokeswoman said.
An ODT reporter at the scene said there were six boats, including some from Dart River Adventures, on the water searching while a helicopter was on a sandbank near the wharf.
Alongside police and paramedics at the foreshore, tourists and locals could be seen on the wharf taking photos in a state of confusion.
It was a nice day with little wind and one local said nobody knew what was happening until they saw the helicopters, the reporter said.
A fisherman who was at Greenstone when the incident was reported had taken part in the search.
He was “gobsmacked that anything could happen here,” the fisherman said.
The water near where emergency services were called to was basically waist deep, although there was a drop-off which could catch people out, the fisherman said.
Police were unable to provide further updates last night.