Pete Bullen said the ministry's decision was a "waste of time to implement", and came down to a "dollars and cents" approach, which pitted schools against each another.
Enforcing a home enrolment scheme would effectively limit the future choice of parents to send their children to the school they wanted.
However, the Ministry of Education's southern district manager, Katheryn Palmer, said a home enrolment scheme would ensure Wanaka schools each had a defined catchment, rather than pitting them in opposition.
She said the decision to implement the scheme was made in response to an Otago Daily Times article, which quoted Wanaka Primary School principal Wendy Bamford.
Dr Bamford was concerned classes would have to be taught on near-by farmland if growth continued at present rates.
"Clearly, Wanaka School has concerns over the ability to manage its growth," Mrs Palmer said.
"Our response to this has been to ensure that Wanaka School can manage future growth by allowing students in its zone guaranteed enrolment. Those from further afield will have the right to attend other schools."
Mr Bullen said the ministry's claims did not make sense.
There had been no consultation and he was baffled that the issued directive was made in response to an article.
Children outside the proposed Wanaka home enrolment scheme would not "have a right" to attend other schools; they would "just have to", he said.
Usually, a home enrolment scheme was directed by the ministry when there was an imbalance in the roll numbers between different schools.
This prevented parents from sending their children to one school, while roll numbers at the other school languished and created an imbalance in classroom space, and ministry funded teaching resources, Mr Bullen said.
This was "certainly not" the case with schools in the greater Wanaka area, he said.
The two other schools in the area - Hawea Flat Primary School and the Catholic-founded Holy Family School - have growing rolls as well.
Mrs Palmer said the enrolment scheme was a mechanism used by the ministry to manage the growth of all the schools in the Wanaka area.
"Hawea Flat School has had an enrolment scheme since 2007 and Holy Family School is in the process of establishing one."
Dr Bamford said she was also confused why the ministry saw the need to implement an enrolment scheme when the rolls of all other schools in the area were rising.
"I can't see the purpose."
However, the school had been instructed to put in an enrolment scheme and "that is what we are doing".
