The Education Ministry says charter schools are getting a total of $888,000 more than they would if their funding were strictly based on their enrolments.
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Seven of the nine schools had fewer students in September than their guaranteed minimum roll, meaning they are being paid for students they do not have.
The ministry said it was not unusual for new schools to be paid for more students than they had.
It said a new state secondary school in Auckland was in a similar position, getting about $800,000 more than it would if its funding were roll-based.
But teacher and principal organisations are not happy.
They say the charter schools have an incentive to stay small so they can get as much funding per student as possible.
Schools assured govt they'd meet targets
Documents show four of the seven charter schools that fell short of their minimum enrolments this year had assured the government they would reach or get close to the figures.
For the second year in a row, the government has funded charter schools for more students than they actually have.
Between them, New Zealand's nine publicly-funded private schools were guaranteed funding for at least 860 students this year.
The Education Ministry had been paying the seven publicly funded private schools, which did not meet their guaranteed minimum, for 669 students, but September enrolment figures showed they had only about 490.
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The owners of four of the schools confirmed they would either meet their guaranteed minimum roll or "be very close", a ministry document said.
The September roll count put all four schools below their guaranteed minimum. However Te Kapehu Whetu-Teina said it recently passed its minimum of 65 and now had 67 students.
Educational Institute president Louise Green said paying charter schools for more students than they had was not on.
"The charter schools are totally different, these are being set up where there are spare capacities in local classrooms," Ms Green said.
"That effectively means that dollars are being taken out of school coffers and those are the very same schools that are crying out for extra resources to support kids with real needs."
The new charter schools were falling short of enrolments because most people were happy with their local state school, she said.
Vanguard students leaving for work or tech courses
Vanguard Military School started the year with 141 students - just shy of its guaranteed minimum of 144. But, by this week, it had just 86.
The school's chief executive, Nick Hyde, said it was not as bad as it sounded.
"As soon as they graduate, a lot of the kids, once they gain their [NCEA] Level 2 qualification or Level 3 qualification, they're looking to go straight into work," he said.
"So we've had a lot of students leave and go into the trades, lot of construction work on the Waterview tunnel, local business have taken quite a few, hotels, obviously the Defence Force is another one, and they also look to do courses at AUT and Unitec."
But that is likely to anger principals and teachers in regular state schools, that lose funding for students who leave them.
However, Mr Hyde said the whole point was that Vanguard was not a state school.
"We're not really comparing apples with apples. We are designed to be a different school, to use innovation, and we feel that if a kid has got their NCEA qualification [and] they are not likely to return next year or do the external exams, why are we keeping them at school?"
Charter funding will reduce over time - ACT
ACT's David Seymour is the Parliamentary Under-Secretary to the Minister of Education and has some responsibilities for the charter schools programme - a policy initiative that the ACT party helped introduce in 2011.
Funding for charter schools would be reduced over time, just as funding is for state schools, Mr Seymour said.
Te Pumanawa o te Wairua, in Whangaruru, Northland, was one of the original five charter schools and was funded for a guaranteed minimum of 70.
"They have not done well retaining students in their first year and their guaranteed minimum role has been dropped to 40, so they're funded for 40," Mr Seymour said.
Some charter schools had more than their guaranteed minimum, while others had fewer students. The numbers would be revised in time, he said.
"There is no story that partnership schools are funded more generously than state schools, as the teacher unions who are relentlessly negative about this policy would like to say - it is simply not true."
The Villa Education Trust runs two charter schools.
Their academic manager, Alwyn Poole, said the first, a middle school in South Auckland, was in its second year of operation and had 120 students - just above its guaranteed minimum of 115.
He said its new school in West Auckland also had 120 students but that was 40 shy of its guaranteed minimum of 160.
"The guaranteed minimum roll isn't necessarily a target - it's what we negotiated with the ministry is a roll that we're able to run our model on. But yeah, we would like more children than that and we're working through those processes now and we would expect to have more children next year."
State schools were also funded to a guaranteed minimum number of students and they were more expensive to set up than charter schools, Mr Poole said.
"Partnership schools get something like 10 percent of the state school set-up and, when you're beginning a school, so for instance you take a Hobsonville Point School or something like that, they receive a remarkable amount of set-up and up-front funding for the first few years while they grow into it," he said.
"But I guess the spotlight's on the partnership schools because people point it that way."
Three other charter schools were set up this year and none of them have reached their guaranteed minimum numbers of students.
Pacific Advance Senior School is the furthest off the pace, with 58 students in September compared to a guaranteed roll of 100.
Post Primary Teachers Association president Angela Roberts said charter schools should not be paid for students they did not have.
"Given that we're constantly being told there's no more cash to go into the system for state schools, that hurts," she said.
"Charter schools are incentivised to keep their rolls down because of the baseline funding that they receive. It's another really good example of how this policy is a complete mess."
Ms Roberts said the government should be using the money it spent on charter schools to provide extra support for children in the state system.