Academies say they are hampered by the "whims of quangos"
Academies are facing a serious erosion of their independence, says a letter of protest from an organisation of these flagship state schools.
Writing to Schools Minister Jim Knight, the Independent Academies Association says they are being made dependent on the "whims of quangos".
They warn of "growing dismay" that England's Academies are increasingly coming under local authority control.
But Mr Knight said the government was protecting Academies' independence.
The Conservatives' children's spokesman, Michael Gove, said his party would make it easier to create more Academies.
He accused the Children's Secretary, Ed Balls, of shifting position on Academies to "curry favour with left wingers ahead of a Labour leadership campaign".
The Independent Academies Association is a representative body for Academy principals and chairs of governors, comprising most of those opened so far.
The letter from its chair Mike Butler says there has been a shift in policy towards Academies, increasingly making them answerable to local authorities and children's services.
"It is with growing dismay that those of us within the Academies movement have witnessed government's changing tack over the last 18 months or so," he writes.
Academies were launched as a way of regenerating educational opportunities in deprived areas, having the support of external sponsors and autonomy from local authority control.
The separation from councils was intended as a fresh start in areas with a long record of underachievement.
But the letter from the Independent Academies Association accuses the government of backtracking on this independence and claims that there is a risk of Academies being hemmed in by "the vagaries of local bureaucracy".
It describes as "deeply disturbing" the current education legislation going through Parliament, which it says will extend the power of local councils and mean "forced collaboration" with children's services.
It also warns that local authority control over post-16 provision could threaten sixth forms in Academies.
Mr Butler warns that the "ethos of dynamism" in Academies requires a freedom to innovate.
The Schools Minister Jim Knight rejected the claim that the government was retreating from the independence of Academies.
"We're clear that Academies' independence and freedom to innovate is absolutely key to their success, which is why we will continue to protect them," he said.
"These freedoms allow Academy leaders to challenge traditional thinking and help make a complete break with cultures of low aspiration, introducing a new ethos and enriching the curriculum."
The government has announced plans to have 400 Academies.