The school has improved safety processes and will pay compensation to the injured students.
One boy had his arm badly injured by the support boat's propeller and the other suffered a head injury.
The coach, Fred Strachan, has retired as a rowing coach and is no longer involved with coaching at the school.
Both the school and Mr Strachan were charged by Maritime NZ under section 65 of the Maritime Transport Act, relating to dangerous use of a vessel.
Maritime New Zealand accepted a submission by the school's defence counsel that as a Crown Organisation, pursuant to the Crown Organisations (Criminal Liability) Act 2002, the school could not be charged under the Maritime Transport Act.
Maritime NZ then engaged in resolution discussions with the lawyers acting for the school and Mr Strachan.
A settlement offer was accepted that Maritime NZ believes achieves an outcome consistent with what a court is likely to have ordered. It has a focus on ensuring that safety improvements are made and the school makes appropriate financial recognition for the physical, emotional and financial harm suffered by the victims and their families.
As a result of this settlement, the charge against Mr Strachan was also withdrawn.
Maritime NZ general manager maritime compliance Harry Hawthorn commended the approach taken by the school's Board of Trustees which had resulted in safety outcomes being achieved without court action adding to the stress of victims.
"We welcome the fact that both the school and Mr Strachan have accepted full responsibility for the accident. We consider that the resolution agreement developed by the school achieves the objectives of Maritime NZ's compliance action without the need to go through a court process, which can be very distressing for victims," Mr Hawthorn said.
"We wanted to ensure that the serious effects of this accident on the victims were acknowledged, safety processes were put in place to protect future rowing participants, and that lessons learnt in this case were highlighted. That has been achieved."
The accident happened after Mr Strachan, who was standing up, knocked the vessel's throttle lever, causing the boat to accelerate sharply.
Mr Strachan fell backwards and the out-of-control boat hit the rowing eight.
Both the school and Mr Strachan have acknowledged that failure to use a "kill switch" system, and the fact that Mr Strachan was alone as skipper and coach aboard the support boat were factors leading to the collision.
