The next stage of school workforce reforms, including providing cover and guaranteed non-contact time for teachers, could be jeopardised following the decision of the biggest support staff union to suspend its involvement in the deal.
Unison activists defied the Government and their own leadership by voting to pull out. They will shun the agreement until national pay and conditions for support staff are negotiated - and have threatened industrial action if they are not.
The vote, at Unison's annual conference in Bournemouth this week, has been greeted with dismay by other unions signed up to deal - the only example of New Labour's much-vaunted "social partnership" approach to industrial relations.
It leaves ministers trying to implement a flagship education policy, supposed to reduce teacher workload and improve support staff pay and conditions - without the backing of the biggest teaching and support staff unions and with the largest headteachers' organisation also threatening withdrawal over funding.
Aspects of the deal already in place, such as the transfer of more than 20 administrative tasks from teachers to support staff, are unlikely to be affected.
But the next two phases of the agreement, a 38-hour-a-year limit on the time teachers can spend covering for absent colleagues, due in September, and the introduction of guaranteed time in the school day for teachers to plan, prepare and assess from September 2005, may be more difficult.
Both require support staff to play bigger roles as either cover supervisors or higher-level teaching assistants and if Unison is not participating then some schools will be unable to negotiate their duties and pay.
John Dunford, Secondary Heads Association general secretary, said: "I think it will cause problems in a limited number of schools where Unison is strong."
Delegates heavily defeated a motion praising the deal as a "breakthrough" for members by 422,272 votes to 253,822. They went on to back a series of motions, highly critical of the agreement, by similarly large majorities.
Christina McAnea, the union's head of education, said: "Unison has said all along that unless the agreement is fully funded, it will collapse."
It was now in the Government's interests to come up with a deal that Unison could support, she said. David Hart, National Association of Head Teachers general secretary, faced a similar rebellion from his members in May when they threatened withdrawal over funding. He said Unison's vote was "potentially very damaging".
But Doug McAvoy, general secretary of the National Union of Teachers, which has been opposed to the agreement since it was first signed in January 2003, welcomed Unison's decision and called on it to join the NUT's campaign against the deal.
The Department for Education and Skills said it remained determined to press ahead with the agreement.
What they decided
Unison conference's view on the workload deal and the action backed by delegates
* The deal has been "largely negative and counterproductive" for members because of under-funding and has "not resulted in any major improvements in pay and conditions".
* Unison should re-negotiate the agreement, drawing up a national pay claim and proper career ladder for all support staff with an end to term-time only contracts.
* A campaign to demand extra resources including, if necessary, industrial action should be launched if the Government refuses to negotiate.
* Heads are "driving a coach and horses" through the deal and Unison is losing credibility for signing it.
* Unison should suspend its involvement in the implementation of the agreement until it becomes compulsory for schools and local authorities to reach agreement with unions on support staff pay and conditions.
* The deal should not be accepted in schools where assistants had been made redundant or had their hours cut because of funding problems.