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A Go Orange jet-boat was carrying 23 passengers when it became beached about 10.45am near the Chard Farm winery and the AJ Hackett bungy bridge.
The Queenstown Lakes harbourmaster was informed and emergency services crews from Arrowtown and Frankton attended the scene.
Go Orange acting general manager Russell Thomas said four people were treated at the scene for minor injuries and one was taken to hospital for further assessment.
Those affected by the incident were being given support, he said.
"Our immediate concern is for our passengers and staff involved."
The cause of the accident is not yet known.
Mr Thomas said a full review of the incident would occur and the company was working closely with authorities.
"The safety of our visitors and staff is a priority in everything we undertake."
The company offers trips from Queenstown, down the Kawarau River, past the Shotover River and back again.
The website boasts it has jet-boats with twin V8 engines that can speed down "the K-river at speeds of up to 95kmh".
Go Orange also offers rafting, 4WD, kayak and cruise trips in Queenstown, Milford Sound, Doubtful Sound and Te Anau.