The PPTA says advice offered by the Ministry of Education to Education Minister Anne Tolley in a report in May last year is "deeply concerning".
After months of official information requests and letters to the ombudsman, a review of the alternative education system was released to the PPTA late last year.
The Findings of Review of Alternative Education and Future Directions document suggested closing alternative education centres and reintegrating troubled pupils into secondary schools.
It said alternative education programmes' links to schools were weak and produced low rates of formal qualifications.
The options put to the minister were to maintain the status quo or "we would discuss with schools new opportunities to get better value for money from the funding [about $23 million] currently supporting alternative education/activity centres," the review said.
"There is the potential for new models to give schools increased responsibility, flexibility and choice in how they assist at-risk students."
Mrs Tolley opted to order the ministry to do further work.
In October, she released a statement saying alternative education contracts with schools would be extended for 2010, but there would be some changes this year as a result of the review.
Yesterday, a Ministry of Education spokeswoman said the review would be considered as part of the wider strategy to keep pupils in school.
At present, secondary schools can refer pupils who have become alienated at school to alternative education or activity centres.
Pupils spend from one term to two years at the centres, with the aim of helping them identify and achieve their goals, including returning to mainstream schooling, attending tertiary training or finding employment.
Up to 3500 pupils access alternative education each year through centres across the country.
The Phoenix Centre in Dunedin, which recently learned it will be closed after a review that cited major issues with systems and processes, is not an alternative education centre, but an "extra support centre".
However, that was "semantics", PPTA senior vice-president Robin Duff said.
The centre provided the same service as alternative education.
"As far as we can see, it certainly sits under the broad heading of special education."
The findings of the review deeply concerned him, he said.
The greatest concern was that it suggested school-based intervention instead of alternative education centres, but provided little substantive advice on how to do that.
"They claim they can put kids back in mainstream school with some kind of ill-defined support. I don't think it's a reasonable thing to be closing centres before something else is in place."
The ministry seemed to think early intervention, high expectations of pupils, good relationships and national standards would remove the need for alternative education, when the people on the ground knew it would take much more than that.
"For a significant minority of kids, up to 5%, without these kinds of small places where they can get personalised attention in a safe environment, they're going to fall out of the education system."
