If passed, the reforms will spell out in law for the first time the right of school staff to punish pupils, confiscate their possessions and use reasonable force, countering what the Government has dubbed the "you can't tell me what to do" culture.
But the Lords and Commons joint human rights committee says the power to use force is "very broadly defined" by the Bill and might risk breaching the European Convention on Human Rights.
The committee's report, published this week, warns that the confiscation of inappropriate items such as mobile telephones, and compelling parents to ensure pupils stay at home during the first five days of an exclusion, could also breach the convention.
It also says that the human rights of pupils at academies and city technology colleges will be less well protected than those at other state schools, because the Government has not made clear that they are public bodies.
The Department for Education and Skills says the Bill will not contravene human rights legislation.
Concerns over the semi-independent trust schools, which are at the heart of the reforms, were a major reason for 52 Labour backbenchers rebelling at the Bill's first parliamentary vote in March.
Trust schools will control their admissions and could be run by private companies.
The rebels will be powerless to defeat the Bill next week as ministers will again be able to rely on Conservative support.
David Willetts, shadow education secretary, said: "There obviously are political temptations to come in and exploit the problems Tony Blair is experiencing.
"But we should not allow politics to get in the way of what we think is the correct policy for education."