Alison King, chair of the Local Government Association's children and young people's board, said limiting council control of schools could discriminate against disadvantaged children.
The white paper sets out a new role for councils as commissioners, not providers, of services and heralds the end of local authority-controlled community schools.
Mrs King believes this will undermine the Government's Every Child Matters drive to improve youngsters' health, safety and economic well-being by limiting co-operation between schools and other services.
Asked whether greater school autonomy could put the detection of child abuse at risk, she said: "I would certainly hope not, but the greater the gaps between services the more likely things are to slip through the net.
That is what Every Child Matters was intended to avoid."
It is a charge dismissed by the Government. But senior figures in Downing Street and the Department for Education and Skills admit privately that greater school autonomy poses a risk to the children's agenda.
They are sensitive to the charge made by children's charities that the white paper divorces the Every Child Matters agenda from the school improvement strategy.
Why should the Government's new "independent" schools put their league table position at risk by taking a greater proportion of difficult pupils and expending limited time and money to collaborate with social services?
The Government's answer is a mixture of persuasion and pressure. Shorn of powers to control schools, councils should attempt to convince heads of the merits of the children's agenda by emphasising the benefits of co-operation with local children's services.
Meanwhile, those who refuse to work with other services will be found out when Ofsted visits.
This approach raises a number of questions. If local authorities fail to persuade individual schools of the benefits of the children's agenda, does this mean a delay to key changes promised as part of the official response to the tragic death of Victoria Climbie?
Will parents care if inspectors criticise their middle-class school for doing little to support children with problems commonly associated with disadvantaged backgrounds? Or will they merely be relieved to see the great unwashed go to another school further across town?
Mrs King, Conservative leader of Norfolk council, said: "This is an autonomy too far. A poor child with a disastrous family background and a disastrous education background and all the problems that go with that will be further discriminated against.
"Sometimes you need a strategic authority with the necessary clout to ensure equity of treatment."
Children's AGENDA 29