CPR was performed on one of the rafters and a defibrillator was used but they died before a rescue helicopter arrived at the scene.
"Challenge Rafting wish to offer their deepest sympathy to the victim's family and friends," she said
Earlier police confirmed that two people were receiving medical treatment following a rafting incident.
Mountain Scene reported that two patients were being treated by paramedics after a raft overturned on the Shotover River.
Emergency services had rushed to Skippers Canyon following reports someone was in the water.
A police spokesman confirmed St John paramedics attended the scene and two people had received medical treatment.
Skippers Canyon is at the head of the Shotover River, a famous destination for thrill-seeking tourists wanting to try bungee jumping and jet boats.
Staff in the offices of tour operators Skippers Canyon Jet and Canyon Swing said they were aware that an emergency response was underway but did not have further details.
The death is the second rafting tragedy to occur on the river this year.
In March, "well loved and highly respected" whitewater rafting guide, Keith Haare,
died in the Shotover River after his raft overturned with other people on board.
Queenstown Rafting manager Luke Taylor said at the time the passengers on the raft were all unhurt and made it to the shore safely, but the company's guide was found unresponsive in the water after attempting to right the craft.
In 2008, a Chinese tourist in her 40s was trapped under a jet boat after it flipped on the Shotover River.
In 2001 a woman died on the river when a raft hit a boulder and overturned. Yoly Chi was trapped in the raft and didn't survive the incident.