All GP practices will be charged an annual fee to fund the cost of registration with the Care Quality Commission (CQC) from 2012.
The body will consult on the annual payments, but a spokesman confirmed that the CQC aimed to 'cover all (registration) costs from fee income'.
The charges come despite the watchdog already enjoying substantial funding, with an operational budget of £166.8 million for 2009/10.
CQC director of registration Dr Linda Hutchinson said registering the 8,500 GP practices in England would be 'an enormous logistical task' and was difficult to cost.
'There will be an annual fee but we don't know how much - hopefully it will reflect activity. We have struggled to assess costings of even (the registering of) the trusts, let alone all the other bodies,' added Dr Hutchinson.
From April 2011 GP practices, alongside all other health and social care organisations, will be required to meet 16 essential standards of quality and safety as part of the CQC's registration system.
The body will have the power to suspend registration in poorly performing practices until these issues are resolved.
GPC deputy chairman Dr Richard Vautrey said the CQC was looking for the profession to fund something that should be paid for by the taxpayer.
'This is similar to the establishment of Postgraduate Medicial Education and Training Board, where registrar trainees bear the cost of the process. It is one thing we are going to need to discuss - how any fee will be reimbursed to practices.'
Asked whether GPs could simply boycott the payment, Dr Vautrey said: 'The problem is they are caught between the devil and the deep blue sea - they will really have no choice.
'CQC registration will be a statutory requirement and GPs' livelihoods will depend on it.'
Dr Vautrey said that something similar to the current mechanisms used to reimburse GPs for GMC and medical defence organisation fees could be explored.
Dr Brian Balmer, chief executive of Essex LMCs, said he would resent paying any sum on principle.
'The GPC needs to look at this. The government is bringing in additional regulation, which I happen to support, but then saying we will have the pleasure of paying for it.
'Money is short, so there is no figure I would consider throw-away. And this is a blank cheque - what will it dream up next? A floor inspection? A health and safety inspection that we have to pay for? It seems a cheek and I think people will resent it.'
In August, GP revealed that the DoH will not fund revalidation annually, prompting concerns the profession will also bear the costs of that scheme.
Dr Hutchinson also revealed that there is still 'a big internal debate' over how much information from the CQC's ongoing monitoring of practices will be made public.