The Government, with Conservative approval, has rebuffed attempts to prevent academy schools becoming exempt charities, no longer regulated by the Charity Commission.
In a Commons debate on Monday, schools secretary Ed Balls rejected a call from the commission to remove a clause from the Children, Schools and Families Bill that would make the schools exempt.
The commission's concerns were raised during the debate by Labour MP Tom Levitt, chair of the All-Party Parliamentary Group on the Community and Voluntary Sector.
The commission had sent selected MPs a strongly worded briefing before the debate, setting out the regulator's view that removing the necessity for the schools to register with the commission and demonstrate public benefit was a "retrograde step, at odds with the direction of Government policy on exempt charities".
But Balls said exempting schools from registration was necessary to make it easier to set up and run academies.
"It is a sensible piece of deregulation and a reduction in bureaucracy," he said. "We now have a large number of academies, with the figure heading towards 400, and the separate and independent regulation of each academy would be bureaucratic for academy sponsors, for accredited schools groups and for the school system."
Michael Gove, the Conservative Party spokesman for children, schools and families, supported Balls's stance and said he had made a "superb case" for academies becoming exempt charities. The measure also received support from other Tory MPs.
A Liberal Democrat motion to reject the bill was defeated. Jenny Willott, the party's spokeswoman on charities, condemned the measure. In a press statement, she said: "Labour is trying to protect its own creation from the high standards of accountability and transparency that apply to everyone else in the sector."
Balls said Angela Smith, the third sector minister, had proposed that academies be regulated by the Young People's Learning Agency, a new government agency that will help local authorities commission education and training for 16 to 19-year-olds.
Andrew Hind, chief executive of the Charity Commission, said he was keen to work with the Department for Children, Schools and Families to find a resolution. "It is imperative that charitable academy schools remain within the mainstream charity framework, so there are no doubts about their status, accountability, transparency and independence," he said.