The Department of Constitutional Affairs said that private providers would not need to share such information with the public, even though standard GP surgeries have to.
The Freedom of Information Act allows private companies not to publish information that might be 'commercially sensitive', such as performance under the quality framework.
The GPC has written to the DoH to complain that this will create an uneven playing field between GPs and private providers bidding for alternative provider medical services (APMS) work.
GPC chairman Dr Hamish Meldrum said: 'We're asking if all contracts can contain clauses saying they will provide information that would have to be provided by any other NHS organisation.'
The GPC is writing detailed guidance on APMS contracts because it thinks there are a number of other areas of difference from GMS and PMS that GPs should be aware of.
GP-led firm ChilversMcCrae published quality scores last year for the practices it runs, but has since formed a strategic alliance with private company Mercury Healthcare, which means they might not do so next year.