"I saw a comment that the money should have been spent on books. That's an old way of looking at learning," she said.
"You can't learn about waka in a book. And we are sitting on the harbour so it would be silly not to use it."
Charter schools, officially called partnership schools in New Zealand, are publicly funded but privately-run.
He Puna Marama is considered by government as a successful example of the model, used most recently by the Productivity Commission as a case study of why New Zealand should privatise social services.
It gained favourable NCEA marks last year, with at least 85 per cent of students achieving across all NCEA levels.
However, the trust has drawn criticism from the Labour Party and teachers' unions, who say its schools are funded at a higher rate than state schools, which is unfair.
The secondary school, Terenga Paraoa, received $1,008,510 in base funding this year, plus a $379,318 student grant. That works out at almost $20,000 per student. Ministry figures show at state secondary schools students get on average $7600 per student per year.
Post Primary Teachers' Association president Angela Roberts said she found the waka purchase "frustrating".
"It breaks my heart, because I know for a fact there are outdoor education teachers in state schools around the country trying to motivate the same kids as He Puna Marama are and they don't even have the money to buy a couple of plastic kayaks," she said. "That's what hurts.
"If there's enough spare cash in the system to spend $100,000 on a waka for a few kids, where's the rest of the money for the rest of the kids who deserve first-class support as well?"
New Zealand Education Institute president Louise Green said state schools would love to have that much money at their disposal - it would buy a lot of support for children with special needs, for example.
"One hundred thousand dollars is an eye-watering amount to spend on anything in a school, and questions definitely have to be asked about this expenditure and whether it is public money that is being spent," she said.
"If the charter school sponsor has enough funding for this kind of purchase, one would have to ask why they are taking public money at all from the education budget, when it is desperately needed in state schools and kura to support children's learning."
Ms Tipene said the trust had several revenue streams aside from its partnership school funding, including ASB grants, its early childhood centres, and social service contracts.
He Puna Marama was hopeful it would be able to design programmes around the waka to enable other schools and youth groups to use it as well.
Costs up to $30k per student
New figures show charter schools are costing up to four times more per student than at state schools — with the most expensive priced at $30,000 for each student enrolled this year.
Numbers released on the nine charter schools also reveal the privately run, publicly funded schools are getting hundreds of thousands of dollars worth of property and insurance money despite some having tiny rolls.
Secondary schools are the most expensive, with the highest price tag at troubled Te Pumanawa o te Wairua in Whangaruru in Northland, at $30,000 for each of its 40 students.
Ministry of Education figures show the average cost per student at a state secondary school is $7600. The primary and middle schools were closer to the average state school cost of $5800 per primary student, with Te Kura Maori o Waatea priced at $7184 per student and Te Kapehu Whetu costing $6995 for each child.
The charter school per-student figures do not include property or insurance, or central funding. In some cases the schools were getting up to $600,000 per annum for property.
Charter schools are much smaller than state schools - the smallest has just 40 students.
Labour MP Chris Hipkins said the figures showed the money was "nowhere near" what state schools received. "But the Government will keep pumping money in to charter schools [in their desperation for] positive results," he said.
The Ministry of Education said costs were expected to come down as the partnership schools grew.
