Shelley Morse wants Education Minister Karen Casey to scrap her plan to have teachers use their professional development days during their vacation instead of the school year.
The 10,000-member union is also opposed to Casey's promise to remove principals and school board administrators from the union, she said.
Casey said the two issues will be dealt with through negotiations with the union, which is getting ready for contract talks this spring.
The eight professional development days are guaranteed in the teachers' collective agreement, but Casey said they should not be part of the 195-day school year.
"One of the concerns that parents have is that (professional development days) ... are disruptive when students are off," she said.
Morse said Casey's suggestion to take the professional development days outside the school year won't work.
"If we need to have math in-servicing, we would like it done during the school year when we are actually teaching the math," she said.
As for removing principals and administrators from the union, Casey said a recent report from an expert panel concluded that parents were concerned about having school supervisors and teachers in the same union.
Casey said that arrangement is virtually unheard of outside of Nova Scotia.
There are dozens of other changes proposed in Casey's sweeping 50-page report, but many of them won't happen unless the teachers' union agrees.
The minister said she wants to draft policies that will set provincewide standards for homework and a classroom code of conduct but she declined to offer details, saying teacher input was needed.
However, Casey said she is committed to having the province's auditor general investigate Nova Scotia's eight elected school boards.
Michael Pickup will examine how the boards are structured and how they spend public funds, she said.
Over the years, some school boards have proven to be so dysfunctional that the government has had to step in to take them over.
Casey said the report released Thursday is important because the latest round of elementary school assessments confirmed a "disturbing" trend: fewer students are meeting expectations in the classroom. The assessments showed that at most school boards, test scores in reading, writing and mathematics had declined when compared with last year.