The council said it had received 500 calls a day - 13,000 in total over the past five weeks - from teachers either confused about the arrangements for payment, or unhappy about the pound;23 charge.
Further problems lie ahead for the council, with the threat of more legal action from the largest teaching union.
On Wednesday, a GTC spokeswoman estimated that 50,000 teachers had replied to a request over preferred methods of payments for the charge. Some 410,000 are required to pay and the official deadline is today.
The spokeswoman denied that the response, which comes after the National Union of Teachers urged its members to hold off payment of the fee, was disappointing. Some teachers had yet to receive their forms and responses were still arriving, she said.
"This is not the final total. It is roughly what we would expect at this stage," she said. Teachers refusing to pay their fees will have them deducted from their salaries in February.
The council is also fighting an increasingly bitter turf war with unions. The GTC could face legal action over what the NUT says are numerous misleading claims in the letters with the payment forms. NUTgeneral secretary Doug McAvoy demands chief executive Carol Adams retract the GTC's claim to be the "new professional body for teachers" and a "membership organisation".
Legislation establishing the council set out its main aim as acting in the interests of the public - not teachers, says the union. The GTC indicated this week that it would not back down.
Briefing, 28-29 The council wrote to all teachers about the fees, its corporate plan and code of practice, last month.
She said the union had been wrong to claim that only 34 of the council's 64 members were teachers. The correct figure was 44.
The GTC has taken on 10 extra staff to deal with fees enquiries which numbered 13,000 in the past five weeks.
Ms Adams said she was "disappointed and surprised" the NUT recommended non-payment.
in an exchange of letters between GTC chief executive Carol Adams and NUT general secretary Doug McAvoy.