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A Fire and Emergency New Zealand spokesman said it was notified at 2.27pm.
A crew from the Otematata station met the boat at the boat ramp and assisted one person who had sustained injuries to his face and head.
A St John Spokeswoman said one ambulance and one helicopter attended.
The injured person was transported to Dunedin Hospital by helicopter in critical condition.
A police spokeswoman said they assisted other emergency services at the scene, near Loch Laird Rd.