The Irish National Teachers' Organisation has rejected the new public service pay agreement negotiated last month.
INTO leadership recommended that their 36,000 members should vote no because the deal failed to eliminate the two-tier pay system, under which those recruited after 2012 were paid 10% less than those recruited prior to that date.
The union this afternoon said 89% voted to reject the deal, with 11% voting to accept it.
It said turnout was 19,172, or 53%.
INTO General Secretary Sheila Nunan, who was one of the four key union negotiators, said the result showed clearly that the terms of the agreement were unacceptable to the vast majority of primary teachers.
She said that while progress had been made in recent years on pay equality, this was not continued in the recent pay talks.
She said there had been an opportunity to draw a line under discrimination and to right a wrong imposed on new entrant teachers - but the proposed agreement did not signal an end to pay inequality.
Ms Nunan also noted that school principals at primary level had been waiting for over ten years for payment of a benchmarking awared intended to reduce inequality between primary and post-primary principals.
The INTO executive will consider the outcome of the ballot next month.
A spokesperson for the Department of Education said minister Richard Bruton noted the decision, and is awaiting the outcome of ballots at the Association of Secondary Teachers in Ireland and the Teachers' Union of Ireland.
The rejection will be seen as a blow to the Government, for whom the extension to the Lansdowne Road Agreement would bring certainty to the exchequer pay bill for the next three years, as well as industrial peace.
However, the rejection by the INTO vote will not necessarily derail the deal, which is expected to pass on an aggregate basis with the support of the two biggest unions, SIPTU and IMPACT.
The big question is whether the ASTI and the TUI will follow the INTO lead and reject the LRA2 proposals.
If they do, it will be the first time in a number of years that all 70,000 teachers in the education sector will be united in opposing a public service pay deal.
That could enhance their leverage in negotiating with the Government.
Both the INTO and the TUI had accepted the original Lansdowne Road Agreement, which was rejected by the ASTI.
ASTI members have lost out on salary and other payments in recent years because of that rejection.
Last week, the Association of Higher Civil and Public Servants became the first union to accept the LRA2 deal when it voted 82% to 18% in favour of it.
Some unions have not yet decided whether to recommend acceptance or rejection, and a number of them will not carry out their ballots until the autumn.
Any unions who vote to reject the LRA2 proposals will have to decide whether they will agree to be bound by a majority vote in favour by other public service unions.
Any unions who refuse to be bound by the proposals will not be entitled to any of its benefits - including pay restoration ranging from 6.2 - 10% over three years.
Meanwhile, the Irish Federation of University Teachers has decided to recommend that its 2,500 members should accept the new public service pay agreement.
It is understood the vote by the IFUT executive was unanimous.
The Garda Representative Association has deferred until September a decision on whether to recommend acceptance or rejection of the new public service pay agreement.
It is understood this is to allow for the preparation of a comprehensive document outlining the pros and cons of the extension to the Lansdowne Road Agreement.
