From 2012, all GP surgeries will be charged annually for registration with the Care Quality Commission (CQC) - the health and social care regulator.
It is not yet known exactly how much practices will be asked to pay, but a spokesman confirmed that the CQC wants to "cover all costs from fee income". The body will consult later on the payments required.
The regulatory organisation is already given substantial Government funding, receiving a £166.8 million budget for 2009/10
Dr Linda Hutchinson, the CQC's director of registration, said it would be difficult to predict the cost of registering practices, as there are 8,500 in England, making the process "an enormous logistical task".
She said: "There will be an annual fee but we don't know how much - hopefully it will reflect activity. We've struggled to assess costings of even [the registering of] the trusts let alone all the other bodies."
As part of the new registration system, GP practices and other organisations administering health and social care will be required to meet 16 essential standards of quality and safety by 2011.
Any surgeries not performing to the required standards may have their registration suspended by the CQC until the issues are corrected.