The GTC claims it is being undermined and pupils will be exposed to risk.
It could lead to as many as 20,000 teachers being allowed to work outside its remit.
There are 12 academies in operation but the Government wants to see 200 up and running, or at least in development, by 2010. The academies, independent state schools set up to raise standards in disadvantaged areas, are part-funded by business sponsors.
Their unusual status within the state system means that teachers will not automatically have to register with the GTC. However, individual teachers may choose to do so, as many already do in the independent sector.
The dispute comes as the GTC revealed that it now had about 490,000, or 96 per cent of the profession, registered and paying the pound;30 annual fee.
Carol Adams, the GTC's chief executive, said: "Academies are a big issue and we have been in correspondence with ministers since the autumn about this.
"Without registration, parents cannot be sure that the appropriate quality assurances will be in place to safeguard their children.
"We do not want people who have been the subject of disciplinary orders in maintained schools turning up in academies. It does not serve the interests of pupils at all.
"We believe in the value of registration as an important safe-guard, which gives parents and the public the assurances that children are being taught by qualified teachers."
The matter will be debated at the GTC's council meeting next week.
Academies have already attracted controversy in their short lifespan, with recent GCSE results revealing that many were performing below standard.
Some have also been at the centre of disputes over the admission of children with special needs, even though they have a duty to accept them if named in a child's statement as suitable.
A spokesman for the Department for Education and Skills said: "Teachers in independent schools are not required to beregistered with the GTC.
However, most of the teachers in academies will be registered with the GTC as they will have come across from maintained schools.
"This is will really only an issue for completely new teachers who start out in academies and this will be a very small number.
"We are in the process of clarifying guidance to academies and we will encourage them to register their staff."