Just before 3pm, Skene and navigator Bruce Harrison, also of Christchurch, were competing in the last leg of the Central Otago Rivers race. It is thought a stone lodged in the steering mechanism or the motor cut out sending the boat out of control.
Witnesses told race organiser Pete Templeton the A-class Eagle jet-boat went up a bank, then 4m in the air, flipped and landed upside down in the water before righting itself.
Mr Templeton said Skene was briefly knocked unconscious and the accident had shown the value of the event's safety protocol. A paramedic on a safety boat at the mouth of the Shotover was at the scene "within seconds."
"It was pleasing to see our safety plan worked well and was able to handle the situation. Unfortunately ... racing at speed these things can happen. I'm just happy no-one was seriously hurt."
Mr Templeton praised emergency workers who aided in the rescue as a bitter, wet southerly front hit the delta.
Both men were taken to Lakes District hospital where they were checked for hypothermia and shock. Skene was also treated for arm and shoulder injuries.
Constable Jason Read, of Queenstown, said police spoke to the men at hospital yesterday.
Queenstown Lakes district harbourmaster Marty Black said an accident report would be filed with Maritime New Zealand by Jetboating Otago but because the accident occurred at an organised sporting event it would not be investigated further.