The other five rafters were rushed to Lakes District Hospital by helicopter, where they were evaluated and offered counselling.
One other patient had injured his shoulder in the ordeal, which was treated by medical staff.
Totally Tourism general manager Tim Barke said the injury was a "suspected dislocated shoulder".
Barke, whose company Challenge Rafting worked with Queenstown Rafting to market the activity, said the company was meeting with the remaining members of the group today.
Following the meeting, Challenge Rafting would also begin to locate the family of the deceased.
"I'm going in with Queenstown Rafting this morning - we're supporting them in any way that we can," he said.
The Queenstown man said a raft flipping wasn't a hugely unusual event, however it was "very rare" for such an incident to result in a fatality.
A statement from the company offered "deepest sympathy" to the victim's family and friends.
"From what I understand they were on a raft, went down a rapid and the raft flipped going through that rapid."
"The customers were brought to the shore, but then something happened and one gentleman needed resuscitating."
He said there was a possibility the deceased may have suffered a medical event.
The company had quite a few Australian customers, he said, who were often "pretty adventurous".
Barke described the incident as a blow to all involved.
"Look, no tourism provider wants anything to go wrong on any trip," he said.
"We really feel for the family of the gentleman involved - it will have been a really traumatic event for everyone."
Challenge Rafting and Queenstown Rafting would be working with police, victim support, TAIC and Maritime New Zealand in an investigation of the incident.
The authorities would also be working to support those involved and the family of the deceased. Police are unable to release the man's name at this stage.
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.
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.