The country's eight charter schools paid their owners or related entities more than $1 million for administration and management services last year.
The schools' financial statements for 2015 also showed most underspent their property funding from the government by $100,000 or more last year.
Under-Secretary for Education and ACT party leader David Seymour said it was up to each of the schools to decide how to use their funding in the best interests of their students.
"What we measure is how much money goes in for education and what sort of educational results come out for the children."
The financial statements showed the eight schools paid the organisations that own them or related companies as much as $360,000 for administration and management in 2015.
Collectively those payments appeared to have totalled at least $1.25m from total funding of about $14m last year.
Vanguard Military School chief executive Nick Hyde said the payments were no different to any other school.
"Take the admin costs of most secondary schools and things like property management, budgets, payroll - we have to do all those things. Usually other schools have a property manager which they pay for, they have someone doing the payroll, they have admin staff," he said.
The South Auckland and West Auckland middle schools are run by the Villa Education Trust.
The schools' academic manager Alwyn Poole said they made payments to the trust for centralised services and management and those payments were higher when the schools were being set up.
"So for South Auckland Middle School in the first 15 months it was $260,000 and that's down to $140,000 and for Middle School West Auckland in their start-up year that was $240,000 and that's down to $150,000 for 2016," he said.
"Those are centralised salaries, and there are four of those, it's centralised accounting services and other admin tasks that go across the schools."
Mr Poole said the organisation was an audited charitable trust and it was not making any profit from the schools.
The financial statements and Education Ministry figures indicate the eight schools collectively received about $3,175,000 for property and insurance last year and spent about half that amount on such expenses.
One of the biggest differences in that spending was in Whangarei where He Puna Marama Trust spent just a third of the $738,000 it received from the government for property for its secondary school and just 18 percent of its primary school's $128,000 property grant, on property expenses.
The trust's chief executive, Raewyn Tipene, said the money that was not used for property last year was being used for building this year.
"The result is a newly built primary school, albeit small, and a central, medium-size city secondary school built inside old buildings," she said.
Ms Tipene said the trust had spent about $4m on property in the past two years and the two schools had been built for a fraction of the cost of a new state school.
Other charter schools were using their property funding to lease premises for less than what the government was giving them for property.
Mr Seymour said it was entirely appropriate for the schools to make savings on property so they could spend more on other education expenses.
He said some were using community resources like fields and swimming pools that were empty during school hours.
"That's what South Auckland Middle School's done and that's a really welcome development. It's certainly not as people have regrettably and cynically described it, a loophole. It's a flexibility and a strength of the policy that they can deploy their resources to get the best outcomes for children."
Post Primary Teachers Association president Angela Roberts said that approach would not work if every school abandoned their fields, libraries and pools and used community resources instead.
She said charter schools, or at least those with secondary students, were able to make their property funding go further because they did not have to provide everything that was required of a state school.
"They don't have to worry about providing an entire curriculum like every other school has to do for example, and they have very small sites. While they may look very entrepreneurial and very flexible at cutting costs, I think there would not be lessons that could be applied right across the schooling network."
Mr Seymour said RNZ should scrutinise the teacher unions and state schools as much charter schools.
But Educational Institute director of campaigns Stephanie Mills said it was important to keep the schools under the spotlight.
"It's important to look at the financials for charter schools because the whole experiment is based on the kind of market idea that if you give these schools the money they'll spend it in the best possible way to get the best possible student achievement," she said.
"Taxpayers have a right to really want to drill down into what's happening there and see if in fact this experiment is working, either from a financial perspective or from the point of view of the students in the schools."
Ms Mills said it was ironic charter schools would use their property funding on other things, when the government wanted to ringfence state schools' property funding.