Baroness Barbara Young said the proportion that would fall short would only become clear when applications began in 2011/12.
But she added that achieving RCGP accreditation would cut the regulatory burden practices would face.
This is because the CQC is aiming, wherever possible, to use readily available information to assess the standard of practices.
Baroness Young added that the process would aim not to be excessively prescriptive.
'We moved away from the approach in the old Care Standards Act where we prescribed the size of a room and what kind of wash basins you had to have,' she told GP.
She also said that practices would face assessment on how well they linked with social care services, and called for more social workers to be based in GP practices.