Academy schools, which were introduced by the Labour Government in 2000, are registered charities, accountable to the commission. But the bill, which has its second reading today, would exempt them from registration and automatically deem them to be charitable.
The 200 existing academy schools would be removed from the charity register and overseen directly by the Secretary of State for Children, Schools and Families.
In a briefing for MPs, the commission describes the move as a "retrograde step, at odds with the direction of government policy on exempt charities". It says the proposed changes would pose a "serious risk of damaging public trust and confidence both in academies and in charity more widely".
The briefing says the spirit of the Charities Act 2006 was to stop the creation of new classes of exempt charities. Under the provisions of the act, many formerly exempt charities are now required to register with the commission.
"The proposals in the bill run counter to this and create exactly the kind of anomaly which the act was intended to eliminate," the briefing says. "This is not just a technical issue. It risks undermining public trust and confidence in the charity sector in England and Wales, which is internationally recognised as being well regulated, accountable and transparent."
The briefing has been sent to party spokespeople on charity and education, as well as to members of the Public Administration Select Committee and the All-Party Parliamentary Group on the Community and Voluntary Sector.
"We have raised these points with senior DCSF officials and are keen to work with the department to find a resolution," the briefing adds.