Mr Wilson said the three men were described as being of Indian descent but it was not yet known if they were locals or visiting Rotorua.
"The group got into some distress and as a result two were rescued by other people swimming in the area. Unfortunately one of the group went under."
He said the Trout Pool area was a reasonably wide part of the river at the bottom of the rapids where the rafters came out.
He said the popular swimming spot was slow flowing and deep.
Mr Wilson said the man's body was found by locals helping emergency services search the area.
Raftabout co-owner Steve McNab said one of his crews were first on the scene to help look for the swimmers after a woman from the group ran up to them and asked for help.
"I was called by the guys because I was back at base. But they told me they dropped everything and went to help. Sadly, it was too late for one of them," Mr McNab said.
"The boys took a kayak down, and then a raft, and started searching. It's pretty deep in the Trout Pool and we understand the swimmer had no buoyancy.
"It's really unfortunate, but a lot of people swim out there, it's not a dangerous part of the river, it's quite slow moving and calm. But quite clearly they could not swim and if you can't swim then any water is dangerous," Mr McNab said.
Rotorua Daily Post photographer Stephen Parker is at the scene and said there was about a dozen people in the area helping emergency services.
He said some were talking about whether there would be a rahui (ban) placed on the river, which was common practice after there had been a death.
An emergency services spokesman said they were waiting for a hearse to arrive to remove the body from the area.
Meanwhile, earlier today emergency services were called to another incident at Auckland's Hunua Falls.
A St John spokeswoman said ambulance assisted an 18-year-old man at the falls.
The St John spokeswoman said it was a near drowning.
The man had moderate but non-life threatening injuries and was not taken to hospital.
- Additional reporting: NZ Herald