Mandatory fees will rise by 10 per cent from April - and teachers will be expected to dig into their own pockets for the first time to cover the rise.
The bulk of the increase, pound;1m, will go towards improving disciplinary hearings and hiring 10 staff as the standard wait for hearings stretches to more than a year.
More employers are referring incompetency cases to the council and the Department for Education and Skills is now passing on more cases of teachers accused of misconduct.
Only 46 hearings were expected this school year but the council has had to budget for 80 and expects 180 in 20062007.
The fee increase is the third since the professional body was launched five years ago.
Teachers receive a pound;33 allowance in their salaries for registration but this is not due to increase. It is designed to cover the current pound;30 fee plus pound;3 for national insurance contributions and superannuation, which vary from teacher to teacher.
David Wilkinson, an NASUWT teachers' union representative, was one of only nine of the GTC's 64 council members to vote against the fee rise.
"This is the first time that teachers will not have the whole fee paid for them," he said. "Teachers do not have a choice, they are coerced into registering."
The National Union of Teachers defended the rise. "Justice is vital," it said.
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