They say more children will be denied the chance to challenge what the local authority provides for them. This is because, after mergers of council services under the Act, the social workers who represent them have to challenge their own bosses.
Social workers are already under pressure to drop cases because a successful appeal costs their council money.
Julia Thomas, from the Children's Legal Centre, estimates that 80 per cent of cases her charity takes up on behalf of children in care are dropped because councils tell social workers to do so.
The senior education lawyer said the conflict of interest for social workers will get worse under the Children Act, which requires councils to merge education and social services.
"In the past there has at least been a division between education and social services," she said. "We have had some courageous social workers prepared to carry cases forward to the tribunal, who have said 'It is not my department so I can afford to push things a little'.
"Now it will mean appealing directly against their new bosses. I think the percentage of social workers prepared to stick their neck out will be even lower than it was before," she said.
She cited the example of a 12- year-old boy with severe learning difficulties who is in care. A social worker acting on Ms Thomas's advice applied for a statutory reassessment of his needs. But when it was refused the social worker did not appeal or inform Ms Thomas. By the time she found out, the three-month appeal deadline had expired.
The local government ombudsman is now investigating the case.
"The Every Child Matters agenda is supposed to improve things for children but could actually make them worse."
Ms Thomas says the solution is to allow children in care to be represented by independent advocates instead of social workers.
A government spokeswoman said it was looking at how to ensure that children in care could benefit from the structures that allow parents to support their children's education.
Children's agenda 29
The Time to Care campaign aims to encourage action to raise the attainment of pupils in care. More than half leave school without a single GCSE.