Learning support managers will start six weeks of industrial action on Monday.
Around 55 staff rejected the Government's latest offer, which included a pay rise of 4 percent and a lump sum of $700.
New Zealand Educational Institute president Lynda Stuart says they feel undervalued.
"What they're asking for really is parity with other Ministry of Education managers, who are currently on far greater salaries than they are."
The strike will include a ban on working overtime and not attending meetings.
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"A ban on attending any meetings, learning support updates, and also a ban on working beyond eight hours a day and working beyond 40 hours a week."
Ms Stuart says staff have been waiting for a better pay package for long time.
"The Ministry of Education was going to be undertaking reviews in this area in 2013, 2016.It hasn't really happened for them."
The strike ends on February 28.