Four other people sustained minor injuries in the accident, which occurred shortly before 5pm.
The injured girl was airlifted to Lakes District Hospital from the crash site near a sandbar in the Shotover gorge.
The five injured were all overseas visitors, Shotover Jet said in a statement this evening. Maritime New Zealand had been informed.
Shotover Jet General Manager Clark Scott said the company's immediate focus was on the wellbeing of its customers and staff.
"Our staff are at the hospital supporting the customers, their families and friends and that's our main priority at this moment in time," he said.
The company was expected to resume operations tomorrow.
In October last year, the company temporarily suspended operations after ''a boat came into contact with a rock''. On that occasion, no-one was injured.
In April last year, the company gained international attention after taking the Duke and Duchess of Cambridge on a trip during their tour of New Zealand.
