In an email yesterday to Labour's shadow children's minister Emma Lewell-Buck, former children's minister Tim Loughton and Carolyne Willow, director of children's rights charity Article 39, Professor Eileen Munro said she has come to the conclusion that the powers could create "more dangers than benefits".
She said there is a risk that a future Education Secretary could use the powers in ways that are "completely contrary to the current intentions".
The email states: "I have been reading the debates in Hansard and the submissions… I've also been meeting with some of those who oppose the bill and I have reached the conclusion that the power to have exemption from primary and secondary legislation creates more dangers than the benefits it might produce.
"While I understand and respect the motivation of the current government, there is a serious danger in having such wide-reaching powers in statute.
"Some future Secretary of State might use them in ways that are completely contrary to the current intentions and consequently subvert the will of Parliament."
Munro, who conducted a major review of the child protection system that was published in 2011, was previously cited by children's minister Edward Timpson as a supporter of the proposals.
In her review, she highlighted concerns about bureaucracy within children's services, something that prompted government to allow a number of councils to take part in a trial allowing them freedoms from statutory guidance.
In the email, Munro said she would back a more rigorous system around exemptions from statutory guidance - something she describes as "a less ambitious but still useful reform".
Carolyne Willow, director of Article 39, has called on the government to drop the proposals.
"The death knell has finally sounded for this appalling attack on children's law and parliamentary sovereignty," she said.
"From the start, ministers claimed their dangerous plan to test out the removal of legal protection from vulnerable children and young people had the backing of Professor Munro. Well, now she has walked away.
"Peers rejected these clauses; more than 50 organisations oppose them; social workers and others with long careers helping children reject them; and more than 107,000 members of the public have signed a petition against them."
A Department for Education spokeswoman said: "We know that over-regulation can get in the way of good social work practice, and the power to innovate will allow local authorities to test new approaches in a carefully controlled and monitored way.
"We have amended these clauses to strengthen the safeguards - to suggest the power to innovate would place children at risk is simply wrong."