Teacher aides who help children learn about recycling, saving water and growing their own food have been scrapped by the Education Ministry because those are not considered "core" skills for children to learn.
More than 600 schools take part in the Enviroschools programme, jointly funded by local councils and the ministry.
A spokesman for Education Minister Anne Tolley said councils could continue funding the programme if they wished but the Government would not contribute.
He said the Government was focused on "core spending priorities" of raising literacy and numeracy and increasing the numbers of pupils leaving school with educational qualifications.
"This programme does not contribute directly to these priorities."
Enviroschools Foundation national director Heidi Mardon said the Government had announced it was breaking the contract worth $4.6 million that was to run from January 2007 to June 2010.
Ms Tolley's spokesman said the programme was worth $19 million over four years.
Ms Mardon said the cut would affect about 20 teaching facilitators who travelled between schools running environment programmes. "Their jobs are gone, as far as we know."
Laingholm Primary in West Auckland is one school that may lose its teaching facilitator. Principal Paul Heffernan was angry about the risk to the programme, which he said had given children the confidence to research projects and present them to the school's board.
"It has turned our school around. You wouldn't get many kids who were confident enough to go to the board of trustees with their ideas."
Mr Heffernan was concerned the roughly 200 Auckland schools taking part in the programme would lose the council portion of funding as well, when the Super City structure came into effect.
Pupils at the school spoke with pride about programmes they had researched, designed, and sometimes convinced the school board to fund.
The school had water savers in its toilets, a pupil-designed proposed fitness trail and raised vegetable gardens outside each classroom, which children judge every two weeks using criteria they drafted.
After lunch, scraps go to a worm farm, are recycled to separate bins and - if kids haven't managed to have a "litterless lunch" that day - anything left over is taken home.
Mr Heffernan said none of those changes would have happened without the Enviroschools co-ordinator keeping the children's projects on track.
Ms Mardon questioned the Government's statement that Enviroschools did not fit with its goal of raising achievement. "We believe it does fit ... and it's probably one of the most cost-effective ways of doing it. For every $1 we are given we raise another $2 elsewhere."
She said the programme would continue, albeit with reduced capacity. Regions would be encouraged to think about how they could pool the facilitators that were left, she said.
"We would like a way forward. We trade a lot on New Zealand's clean and green image and education is a huge part of that."
Government funding for Enviroschools is due to stop in December, affecting about a quarter of all New Zealand schools. Representatives of Enviroschools will meet education officials on June 22.