The move reflects the mood of teachers who have already experienced a two-year pay freeze, increased pension contributions and "excessive" workloads, according to the Educational Institute of Scotland (EIS).
Teachers are being asked to be more flexible in their working week, such as working an extra two hours one week then being paid back with reduced time in another week, the union said.
Concern has been raised that extra duties could fall on teachers, including administration and lunchtime supervisions.
In a consultative ballot, just under 59% of respondents voted against the proposals negotiated through the Scottish Negotiating Committee for Teachers following the McCormac report on teaching employment.
EIS general secretary Larry Flanagan said: "The EIS has been consistent in stating that any proposals arising from discussion of the McCormac report would be subject to a ballot of our members. We have now completed that process and the result is a clear rejection by Scotland's teachers of the suggested changes to working conditions.
"As always, the EIS is listening to its members and will make teachers' views known to the management side at the forthcoming meeting of the Scottish Negotiating Committee for Teachers (SNCT)."
The ballot may also have implications for an agreed 1% pay offer.
"No one wishes to see disruption in our schools, particularly at such a crucial phase in the implementation of Curriculum for Excellence, so we will await discussion of the issues at the SNCT before deciding how to proceed," Mr Flanagan said.
"The ballot result, however, is indicative of the mood of teachers who after a two-year pay freeze, increased pension contributions and in the face of excessive workload have simply said, 'enough is enough'."
Education Secretary Michael Russell said: "I am disappointed that EIS members have voted to reject the proposals.
"Obviously the Scottish Negotiating Committee for Teachers will have to look at this matter as a matter of urgency when they meet tomorrow."