The new zone, due to come into force on February 1, would exclude children living in five Queenstown suburbs from enrolling in the Frankton school, despite community opposition to the restrictions.
The ministry advised the school board it was "unable" to officially approve the new zone, just one hour before the deadline set by trustees on Monday.
The deadline was given to urge the ministry to respond to the concerns raised in 156 public submissions, many of which labelled it a "Band-Aid" zone reduction, and because the board must plan staffing, operational budget and infrastructure needs for 2012.
Board chairman John Stalker said yesterday the ministry told the trustees there were "inconsistencies" with their submissions and the Education Act and "processing requirements" meant it was unable to sign off on the zone.
"They don't believe the policy we've written fully meets the guidelines of the Secretary of Education," Mr Stalker said.
"All they've said is it does not fit within the Wakatipu Area Strategy. They've asked us to check through those things and resubmit it to them by October 14. We wait for them to make another decision."
The board was also waiting to hear from the ministry on its solutions for district-wide population growth and schooling options for the future, he said.
Trustees were "very demoralised, disappointed, frustrated. The whole process just seems to be taking time with little communication from the ministry. There is a lot of planning that needs to be done for next year, particularly the fact that we have years seven and eight starting next year, so there are staffing requirements for that.
