Unison, the biggest support staff union, says another 48 per cent of English and Welsh LEAs had begun negotiating structures to determine pay for support staff taking on more duties under the deal. But 44 per cent had done nothing at all.
The figures are disputed by the Local Government Employers' Association, but even it admits that in 2003 a quarter of LEAs had yet to start planning their structures.
The news came as it emerged that unions in Newham, east London, have defied their national leaders who signed the agreement and advised schools not to impose additional responsibilities on teaching assistants, unless they are paid extra.
Christina McAnea, Unison head of education, said her figures, based on reports from local union officials and employers, were disappointing.
"Until LEAs have got a local grading and pay structure in place it will be impossible for schools to implement the agreement properly," she said.
Nigel Middleton from Head Support, a consultancy helping heads to implement the agreement, said schools needed to decide how to organise their staff and what to pay as their duties expanded under the deal.
"These decisions are not that difficult to make," he said. "But they are impossible to implement if your LEA does not have a pay and grading structure that reflects the new career opportunities open to teaching assistants."
In Newham, support staff unions say assistants are not being paid by schools for increased responsibilities. They have issued advice, contradicting the workload deal, saying they should not have additional duties imposed on them and should not be asked to teach or take responsibility for whole classes except in exceptional circumstances.
It has been backed locally by the anti-agreement National Union of Teachers and, more surprisingly, all education unions which signed up to the national workload agreement except the National Association of Schoolmasters Union of Women Teachers.
It is an embarrassment for the unions' national leaderships and for Graham Lane, leader of Newham council and education chair of the Local Government Association, one of the signatories to the agreement.
John Dunford, Secondary Heads Association general secretary, admitted the advice contradicted his union's national policy.