Hundreds of teachers will not be registered by the start of the new academic year, meaning that legally they should not be allowed to work in a school.
But both the council and the Department for Education and Skills said this week that they had no plans to take action against unregistered teachers.
Union leaders have accused the council of failing to plan properly for the massive task of registering more than 400,000 teachers in the past year.
The register will underpin the council's key function of disciplining teachers.
The council now has the power to consider cases of teacher misconduct or incompetence. Striking teachers off its register is its key sanction, and schools will check the register when appointing new staff.
GTC chief executive Carol Adams said: "Most of the register is now in place. Any teachers concerned that they're not on the register should contact the registration helpdesk on 0870 001 0308."
In a letter to Liberal Democrat education spokesman Phil Willis, Ms Adams said that the council had received details of 412,797 teachers.
As of two weeks ago, it had processed 87 per cent of these, and anticipated clearing the rest by the end of August. But Ms Adams added that some teachers would remain off the register because the council had not been able to trace them.
The admission brought immediate accusations that the GTC would not be able to police the profession properly if its register were incomplete.
Latest figures from the School Teachers' Review Body indicate there were 421,296 teachers working in English state schools last year, seemingly leaving the register several thousand teachers short.
All qualified teachers working in state schools are required to be registered. The council has spent the past year attempting to collate and check teachers' details, while also seeking to defuse a row over the pound;23 annual fee that is required.
Mr Willis said :"If the GTC is to be the professional body for the teaching sector then the continuing problems with the registration system must be overcome as a matter of priority."