Vice chancellors fear that the creation of a single qualifications authority, heralded in this week's Queen's Speech, could give ministers the power to approve some higher education awards.
Plans to merge the School Curriculum and Assessment Authority and the National Council for Vocational Qualifications into a single body are to be contained in a new Education Bill.
Details of the proposal from the Department for Education and Employment seem to extend the secretary of state's powers through the remit of a new Qualifications and National Curriculum Authority to control approval of higher education awards.
A DFEE press release talks of "an extended power for the secretary of state, on advice from QNCA, to approve the qualifications which can be offered by schools, colleges and other publicly funded training".
An earlier draft of the remit said the new body would "advise the secretary of state on the approval of qualifications for use in wholly or mainly publicly funded programmes of education and training, excluding higher education".
A spokesman for the Committee of Vice Chancellors and Principals said the change in the wording of the remit could cause concern.
"We will have to look at it very carefully to ensure that the thin end of the wedge is not being inserted," he said.
Meanwhile, Bryan Davies, Labour's further and higher education spokesman, warned that measures in the bill to encourage more schools to take up grant-maintained status could prove damaging for FE colleges.
The proposals would help perpetuate small school sixth-forms that are more expensive to run in colleges and will compete with them, he said.
The Liberal Democrats also launched their alternative to the Queen's Speech, containing proposals for a Lifelong Learning and Further Education Bill.
The bill would propose training entitlements for everyone, and the creation of learning accounts to replace the present student loans scheme.