Details of how the council's misconduct and capability procedures will work are still being hammered out by GTC officials, unions and heads' associations.
One of the main sticking points is the make-up of panels which will have the final say on whether teachers are struck off the professional register. The GTC wants the right to co-opt people on to the panels, which could deal with up to 1,000 cases a year.
The council, which will decide who is co-opted, is proposing an open selection process and detailed training for those chosen. It has also given assurances that council members will make up the majority on panels of five or three.
But Nigel de Gruchy,
NASUWT general secretary, claimed this would do little to allay the profession's fears. "Teachers expect to be judged by a group of their democratically-elected peers. Co-options alter the basis on which the GTC was established. It is an unacceptable proposal which will undermine confidence in the process," he said.
The National Union of Teachers has also opposed the move and the heads' associations are uncomfortable with co-option.
ohn Dunford, general secretary of the Secondary Heads Association, said it would be impossible to sustain the required level of work long-term if the panels were staffed entirely by GTC members, many of whom were full-time teachers.
In Scotland, which has 50,000 teachers, 244 teachers were referred to its GTC, of which 12 cases went to an investigating committee. Two were removed from the register.
Carol Adams, GTC chief executive, said: "Our interest in co-opting other members would be if the workload involved in hearing cases was unmanageable and create a backlog, which would be unacceptable."
Ms Adams said the panels would include members from outside the profession to avoid being seen as a protective and inward-looking organisation.
The row has developed as the General Medical Council, the health professionals' watchdog, comes under severe criticism from the public following a number of high-profile incompetency cases.
Calls have been made for the disciplinary body to include outsiders to guard against the accusation of doctors protecting their own.
Disagreement between the teaching council and unions has also arisen on whether the council should take on capability cases where teachers resign before they are dismissed.