The council will also be required to produce a code laying down standards of professional conduct.
But Stephen Dorrell, shadow education secretary, said the council's powers over professional incompetence could be used to hound traditionalist - or trendy teachers - if the way they teach does not conform to the council's standards.
The changes to the Teaching and Higher Education Bill, set out in amendments by standards minister Stephen Byers, were welcomed as a step forward by Liberal Democrat Phil Willis. He said the Government's original plans had reduced the council to a registration bureau, but the Bill still gave the Secretary of State too much control.
Mr Willis argued the GTC, if it is to have similar status to other professional bodies, should be able to set the registration fee.
The council enjoys cross-party support, even from the Conservatives - who opposed the idea when in Government. But MPs were concerned that too many of the details were not included in the Bill and would be decided by the Secretary of State.
Mr Byers said a consultation document on the council would be issued as soon as possible. He said the composition of the body would have to be determined by an affirmation resolution in both Houses.
Teachers will form the majority of the council, and when asked to define what a teacher was, he said only those with qualified teacher status would be eligible. Other categories, for example FE lecturers, could become associate members.
In answer to amendments put down by Mr Dorrell on representation by different teachers from different sectors, Mr Byers gave assurances that all relevant sectors would be included and the Secretary of State may nominate a member from higher education.