Queenstown Lakes District Council harbourmaster Marty Black said the man (20) was believed to have crashed and been knocked unconscious about 4pm on Saturday.
At 8.04pm, the man contacted Queenstown police to tell them he could not find his friend, also 20, who had been riding another jet ski with him before the crash.
A "missing person" call was sent out about 8.30pm and a Heliworks helicopter, Coastguard Queenstown, Queenstown police, two Kawarau Jet jet-boats, and Queenstown Lakes District Council harbourmaster Marty Black began a search and rescue operation on the Kawarau River for the missing man.
However, he was located uninjured at his Queenstown residence about 90 minutes later.
Acting Sergeant Craig Gibson said the man who reported the missing person told police he woke up in the water after the crash, swam to a nearby bank and sat in shock for about an hour before making his way home.
The man was in Dunedin Hospital last night with serious facial and head injuries, and very little memory of the incident, police said.
"It's quite possible they set off separately before the crash and the injured man is the only witness," Sgt Gibson said.
Considering the current climate on Lake Wakatipu, delays were risky and it probably had been best to go in heavy-handed, Sgt Gibson said.
Soon after the distress call, Mr Black began searching the area on his own jet ski and found the badly damaged craft caught up in vegetation on the side of the Kawarau River, about 200m above the Shotover confluence.
"There is a warning here people need to listen to - jet skis are extremely dangerous in the wrong hands," Mr Black said.
Details of the crash are still being investigated, and Mr Black suspects a third jet ski may have been involved.
"If it was a tree or a fence, there would be a trace ... from looking at the markings on the ski, it looks like another jet ski was involved - it looks like metal on metal".
The uninjured male's jet ski appeared scuffed, but not badly damaged.
It had not been confirmed whether it was involved in the crash, Mr Black said.
Both the men are believed to have been wearing life jackets.
The Kawasaki STX-15F jet ski which crashed would have been capable of reaching speeds of about 100kmh.
Mr Black asked for anyone who had seen two red jet skis on the Kawarau River or Lake Wakatipu on Christmas afternoon to contact him or the police.
