Registration fees for GP practices are likely to rise 2.5% in 2014/15 under proposals being consulted on by the watchdog.
For 2013/14, the first year in which practices have had to register with the CQC, they have paid up to £850 each.
But the CQC has said this will need to rise because it is statutorily required to recoup its costs from organisations it regulates, and the current fee covers only half of the necessary amount.
GP leaders fear costs could more than double, however, if the new inspection regime set up to support the CQC's first chief inspector of primary care proves more expensive than current arrangements.
This month, former RCGP chairman Professor Steve Field took up the post on a salary of up to £175,000.
Professor Field said his inspection teams would be 'loaded with GPs', with inspection pilots beginning in December.
GPC deputy chairman Dr Richard Vautrey said any fee rise was unjustified. Based on comments by Professor Field since he took up his CQC role, Dr Vautrey said there 'appears to be a risk' the new model would increase the cost of CQC checks and this would be 'paid for by GPs'.
Dr Vautrey said: 'There is no justification for a rise when general practice is facing unfunded rising expenses that are leading to resource cuts.
'The CQC has a duty to recover its costs, but we have always argued this is in effect an unfair tax on practices, paid for by GPs, unlike other doctors in the health service where costs are borne by the organisation.
'We have also repeatedly expressed concern that this arrangement does not provide discouragement for the CQC to limit its costs.'
A CQC spokesman refused to rule out GP fees more than doubling: 'Later this year, the CQC will be communicating details on the new model for GP practice inspections.
'The government is clear the CQC must recover the cost of regulation from providers. Every time there has been a suggested change in fees, there has been a full consultation - this will continue with any new changes.'