It fears that the First Minister's commitments to smooth the transition from upper primary to early secondary will dilute high-quality teaching in both sectors and erode the core duty of the GTC to protect standards in the classroom.
Matthew MacIver, GTC registrar, told a council meeting on Wednesday that Scottish Executive plans to repeal the next stage of the 1956 Schools (Scotland) Code in 2004 would have "huge implications for the teaching profession".
Ministers had not thought through their proposals which would impact on existing legislation and the professionalism of teachers, Mr MacIver said.
He has already met Peter Peacock, the incoming Education Minister, twice to press home his point.
At present, primary teachers must have a separate qualification and secondary teachers must have an appropriate qualification for their subject. The Executive is to consult on scrapping the restraints.
Mr MacIver is also concerned that a shortage of teachers in certain subjects could be cured by altering the code and "arguably lowering the standard of teaching in the profession".
He said that the significance of removing nursery teachers from a designated role in pre-school education, which takes effect from the end of next month, was now becoming clear. The next stage would be an attack on the primary and secondary sectors.
"The council was set up to ensure that certain standards and benchmarks were adhered to and ensure that teachers were only employed to teach in areas in which they were registered and qualified. That is the council's core business and I feel very strongly that the repeal of regulations would begin to erode the statutory power given to the GTC in 1965," Mr MacIver said.
Legal advice suggested there was nothing to stop the Executive but Mr MacIver said the GTC, by law, was in a position to advise ministers about fitness to teach and supply of teachers.
"It would therefore be open to the council to recommend that teachers should be employed only in the subjects in which they are registered to teach," he said.