For practices with 5,001 to 10,000 registered patients, the fee will increase by £60, to £725 per year. Practices with 10,001 to 15,000 patients will see an increase of £69 to £839 each year.
If implemented, practices would have to pay the inflated fee from 1 April 2015.
CQC spending has increased by £44 million this financial year through the costs of the new inspection regime.
The new inspection regime was launched at the start of the month, and introduced OFSTED-style rating systems for primary care.
A CQC statement said increased fees are the cost of developing a model that “everyone can have confidence in”.
The statement reads: “The fees paid by providers, together with grant-in-aid from the government, are central to ensuring that CQC can carry out the job it is committed to delivering - registering and inspecting health and adult social care providers to make sure they provide safe, effective, compassionate and high-quality care, monitoring them to make sure they continue to do so, and taking action if they don't.”