GPs providing out-of-hours services will be charged in the same 'banding' as dental and ambulance services for registration with the Care Quality Commission (CQC).
This means out-of-hours practices, who will be registered from April 2012, will pay an annual fee of between £800 and £48,000, depending on the number of locations.
'Certain' PCTs will also be charged a flat rate annual fee of £1500 under the new fee structure.
The fees are said to reflect government guidance to CQC that it must recover the costs of regulation from providers.
The changes also follow two consultation exercises by the regulator.
"Our approach to fees is based on fairness and on raising only as much income as we need to cover the costs of regulation," said CQC Chief Executive Cynthia Bower.
"We have listened to what providers have told us during the consultations and have made changes to address concerns and make the fees that we charge transparent and as proportionate as possible."
The CQC will launch a third consultation later this year on its 'longer-term fees strategy' from 2013/16 for GPs and other primary medical services, who will be registered with the regulator from April 2013.