Under clause 68 of the bill, additional powers will be given to learning and skills councils which could override local decision making on sixth-form provision.
The union believes the plan will sow fear among schools with 'small but viable' sixth forms, and regards the proposals as interventionist.
Until now only councils, schools and school organisation committees were able to propose changes affecting school organisation. In future their ability to act would be halted if learning and skills councils proposed changes in sixth form organisation.
He added: 'The proposal for closure would come from a body which will not have the local involvement which is part and parcel of the school organisation committee.'