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Police and St John were alerted to the accident, on the river near Mt Earnslaw, around midday.
The cause of the crash is not yet known, but a St John spokeswoman said two people had been treated for moderate injuries. One was being airlifted to Southland Hospital and one to Queenstown Lakes District Hospital.
Three helicopters were originally sent to the scene but one was stood down.
The Rescue Coordination Centre was alerted after a Personal Locator Beacon was activated at about 11.45am.
The centre said it was leading a response to an incident involving a private jet boat.
Two helicopters with medical capabilities, one from Te Anau and the other from Dunedin, attended.
- NZ Herald/ODT Online