All practices will be expected to register with the watchdog from April 2012. Unless the fee is paid directly by the Treasury, the GPC plans to submit evidence to the Doctors' and Dentists' Review Body calling for funding to cover it.
Dentists were obliged to register from April this year, and pay a £1,000 annual fee.
The rate for GPs is expected to be similar.
Although dentists pay the fee directly, the GPC has argued that dentists can raise additional income in ways that GPs cannot. GPC chairman Dr Laurence Buckman described the registration cost as 'a tax on doctors'.
The CQC system, which requires GPs to meet essential standards of quality and safety, was recently trialled by NHS Derbyshire across 21 practices.
Derbyshire LMC secretary Dr John Grenville said a key problem faced by the pilot practices was limited time to prepare. 'When it becomes real, practices will be given a fortnight,' he said.
He urged practices to prepare for registration in advance and ensure that their practice managers were not away.
Practices should be aware that they 'don't have to present all evidence at time of registration', Dr Grenville said.
Once practices have made a 'self-declaration' the CQC may look into and discuss any plans.
Practices should have a written protocol to prove they are doing what they have claimed, he said.
Dr Grenville predicted GPs would have to pay a registration fee similar to the price for dentists, around £1,000.
Practices operating from more than one site can avoid additional registration fees by appointing a 'single officer' with legal responsibility for their registration, he said.
A CQC spokesman said that it would be holding a consultation over the summer to decide on how registration fees should be paid. The GPC plans to issue a CQC registration toolkit in late May.