The council is facing a pound;900,000 shortfall because it lacks up-to-date records that would enable it to track down the 39,000 of England's 430,000 registered teachers who have not paid.
The revelation comes as the council prepares to raise the fee to pound;28 and despite the Government's decision to put pound;33 into teachers' pay packets to fund the charge.
More than 200,000 teachers refused to pay voluntarily, forcing the GTCE to dock salaries in May.
But Dennis Jones, head of finance and administration, said the council was still trying to track down many teachers who had moved schools recently.
Records dated back to 2000, he revealed, when the register was first collated.
If teachers move schools, employers are supposed to tell the council, so it can deduct the fee. But not all have done so. In addition, it has proved difficult to track some supply teachers, who often only work a few days in a school.
But Mr Jones said: "We will collect the fees outstanding."
The council is increasing its fee following a cut in Government funding.
But it is likely that ministers will continue to boost salaries by pound;33 a year to cover the cost.
The fee is deducted at source in Wales and all teachers have paid.