Emergency services were called to the incident on the Clutha River, near Hawea Flat, about 1.30pm.
The jet boat was part of the annual Otago Rivers Race.
In a statement, police later confirmed that two people were involved and one had died at the scene.
"The other person has received moderate to serious injuries and have been taken by helicopter to hospital."
The Swift Water Rescue team was called out to assist with the scene examination and Maritime New Zealand were also on their way.
Police said the area where the crash happened was difficult to get to, and emergency services would take some time there to establish the cause.
An Otago Daily Times reporter at the scene said a vessel appeared to have been dragged up the riverbank from where it had crashed.
There was no obvious sign of any rocks in the water near the scene, which was at the first sharp bend in a series of bends below Wanaka Airport.
The boat was still in one piece, but it appeared to have been damaged on top.
It is the second serious jet boat accident in the Central Otago/Lakes District area in as many days.
On Saturday morning, nine people were injured after a jet boat operated by Skipppers Canyon Jet crashed into a rock while riding the Shotover River in Skippers Canyon.
A Canadian tourist was flown to Dunedin Hospital after her leg was broken. Eight other people had minor injuries.
An investigation is under way and the company had suspended its operations.
- additional reporting ODT Online
