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The men, from Christchurch and Queenstown, were returning upstream from Lake Dunstan yesterday when the accident occurred.
"It seems that the lead jetski stopped suddenly after the driver noticed a big rock in the river. The other driver either did not notice that he had stopped, or did not have time to take evasive action, and the second jetski rode right over the top of the first one," Mr Black said.
The men swam to shore and the jetskis were recovered from the river before dark last night.
"When you see the damage to the first jetski, you have to wonder how they got away without injury," Mr Black said.
Jetskis and other boats should maintain a safe distance of at least 50m distance from other craft at all times.