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The NZEI union has announced that it will not engage in collective negotiations in an attempt to shape how the reform will take shape.
Ninety-three per cent of its members who voted said they had "no confidence" in the government's plan.
Prime Minister John Key kicked-off National's election year in January with a policy dubbed Investing in Educational Success that will cost an extra $360 million over four years.
The scheme aims to identify the best principals and teachers and pay them more to spend time in other local schools or provide an example within their own.
Schools that are struggling can also ask for an allowance of $50,000 to top-up the salary they can use to attract a principal.
The four new roles would work across a "cluster" of 10-12 schools. Schools that do not want to be involved can opt-out.
The leadership of NZEI has been a vocal critic of the policy, arguing the money would be better spent on helping lower decile schools cope with children damaged by poverty and neglect.
Union president Judith Nowotarski said the policy had proposed a "one-size-fits-all, top down management structure" which would create the most radical shift in schooling since Tomorrow's Schools.
She said the policy had been proposed without the involvement of schools or parents, and with no evidence that the new model would help student learning.
"Principals and teachers at the chalk face want the best possible outcomes for their students, and that means resources to meet their needs.
"It is time for the government to return to the drawing board and come up with something that unequivocally puts children's needs first," she said.
Today's rejection of IES is less likely to be repeated at the secondary school level.
The Post Primary Teachers Association (PPTA) has been working through detail of how the new roles would work with the government, and pushing for some changes.
Its executive has been supportive of IES, and negotiations are ongoing on the teaching roles associated with secondary schools.
In a statement earlier today, Education Minister Hekia Parata said the Ministry had reached agreements with organisations that represent the principals of the 339 secondary schools in New Zealand, as well as the NZ School Trustees Association.
"We remain committed to implementing this initiative with all those groups keen to be involved."
Ms Parata was unavailable for immediate comment on the NZEI vote.