Baroness Barbara Young told GP she would ‘leave it to the government and providers to argue it out', adding that fees could be ‘pifflingly small' or ‘whackingly large'.
‘I don't hold a candle for fees because they don't get us anywhere,' she said. ‘For every pound raised in fees, the government lops it off our grant.'
‘The treasury declares that regulators must recover their costs through fees - end of conversation.'
The CQC admitted last month that it has found it difficult to cost the process of registering England's 8,300 GP practices.
A CQC consultation launched this month suggests practices will face charges for adding a partner or branch surgery, on top of an annual payment.
It says the annual fee is likely to reflect a provider's type and size. Examples given at this stage relate only to hospitals -the smallest hospitals with 50 to 251 beds would pay £15,000 a year for CQC registration.
Flat fees of £2,000 for altering registrations and £5,000 for registering a provider formed after April 2010 are proposed.
However, how this will translate to practices remains unclear. The CQC will begin consult on fees for providers including GPs in Autumn 2010.
All GP practices in England will have to register with the CQC from 2012.