Unions say some councils are failing to play their part in its implementation which should have begun this month.
One, Swansea, attempted to delay implementing the agreement, which involves transferring more than 20 administrative tasks from teachers to support staff, until February.
It wrote to schools in July saying funding problems made the agreement impossible to deliver locally and warning that standards would suffer unless a pragmatic approach was taken. The letter implied unions had agreed to the delay but several have denied their involvement and forced the council to back down.
Dafydd Morgan, National Association of Schoolmasters Union of Women Teachers South Wales national executive member, said: "Our members were aghast. There is no way we would undermine a statutory national agreement."
Pro-agreement unions Unison and the NASUWT, as well as the National Union of Teachers, which did not sign the deal, say some councils are not playing their part in implementing it.
Christina McAnea, Unison head of education, said: "Councils have been very slow in getting their act together. The agreement isn't being implemented in schools yet because heads haven't been getting the advice they need from local authorities."
John Bangs, NUT head of education, said a meeting of local secretaries from across the country revealed a "wide disparity" in what local education authorities were doing to implement the reforms. But all LEAs apart from Sandwell had allowed the union into local discussions, he said.
John Wycliffe primary in Lutterworth, Leicestershire is one of several schools struggling to give teachers more free time in the school day for lesson preparation because its local authority is comparatively underfunded.
Instead of increasing its use of teaching assistants the school has been forced to cut a full-time support staff member. And only one of its 12 teachers receives a half-day of non-contact time each week.
Paul Burlingham, the head, said: "We've done quite a lot to ease workload but teachers are still having to put the pupils before their contracts sometimes - for instance, by getting the support staff to work with children instead of on admin tasks.
"You become cynical about intitiatives that are heralded as a great thing and turn out to be a poisoned chalice."