A 12-year-old Australian girl remained in hospital last night following Saturday's crash, the incident occured when Shotover Jet boat came through a twisty canyon on Shotover River, about 4.30pm.
Five others were injured in the incident - including a honeymooning couple - but have since been released from hospital.
It is the second recent crash for the company. In October, one of its boats clipped a canyon wall on the same stretch of river. No-one was injured in that incident.
An investigation by Maritime New Zealand pinpointed a ''lapse of judgement'' by the relatively inexperienced driver.
Shotover Jet manager Clark Scott said despite two similar crashes, such incidents were ''really unusual''.
''We're a wee bit in the dark, and we want to know. We want to mitigate it ever happening again,'' Mr Scott said, describing it as ''very frustrating''.
''We're pulling our hair out.''
Mr Scott would not go into detail about the factors that led to the October crash, or what measures, if any, had been taken by the company since.
But he said that while rocks had been known to move under the water, ''the environment we operate it is predominantly stable''.
''However, we operate in adventure tourism. The very nature does include an element of risk, and that I think is acknowledged and understood by all within the industry,'' Mr Scott said.
''Any responsible operator - and I put ourselves in that grouping - all we can do is minimise that risk by having in place the best, most comprehensive safety, training and maintenance programmes we can, and we believe we have the best in the industry.
''Further to that, the safety of our passengers and our staff is paramount. If it wasn't for safety, we would not have a business.''
The company, including the male driver, was taking the Maritime New Zealand investigation into the crash with ''the utmost seriousness'', he said, and had brought in an independent investigator of its own to help determine what happened.
Mr Scott said while the driver was a ''newer'' member of staff and not the same driver as in the October incident, he was ''very experienced''. All Shotover Jet drivers had a minimum of 120 hours of training, compared with the industry standard of 50 hours.
The driver has been stood down while the investigation takes place, but Mr Scott said he would be happy to bring him back on board once that was complete.
Shotover Jet resumed operations yesterday morning at 8am, after clearance from Maritime NZ.
The company, which is owned by Ngai Tahu Tourism, has carried more than three million passengers since it was launched in 1965.
In April last year the company gained international attention after taking the Duke and Duchess of Cambridge on a trip.
Additional reporting by NZME.
Previous Shotover Jet incidents
• October 2014 - The company temporarily suspended operations after a boat hit a rock with 10 people on board. No injuries were reported.
• November 2010 - 12 people suffered minor to moderate injuries when a boat crashed into a cliff face.
• November 1999 - Japanese tourist Yuichiro Shibata (30) was killed and 11 others injured when a jet-boat hit a canyon wall.
• October 1999 - Nine passengers taken to hospital after a boat hit a rock. There were no major injuries.
