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The incident took place about 2pm and Queenstown harbourmaster Marty Black said it was highly likely Maritime New Zealand would be investigating further.
Mr Black could not comment further at this stage.
St John Ambulance communication officer Kelvin Perriman said one male and one female were airlifted to hospital with minor injuries by the Lakes District Rescue Helicopter. They were in stable condition.
Queenstown police received a call at the time of the incident but did not attend the scene, Sergeant Phil Hamlin said. The female had complained of a sore neck and was flown to hospital as a precautionary measure.
Maritime New Zealand spokesman Steve Rendle confirmed the two boats were owned by Dart River Safaris. One was carrying passengers and the other was empty.