Government proposals will position clinical commissioning in a "full-scale market" and introduce "commercially-focused criteria" in appointing support staff.
The British Medical Association (BMA) said recent guidance issued by the government will make it "very difficult" for CCGs to employ their own commissioning support staff and for NHS commissioning support bodies evolving from PCT clusters to compete against large, established commercial organisations.
The BMA is seeking an "urgent" meeting with the government in a bid to urge them to reconsider their proposals.
As CCGs will be left with "little choice" but to rely on commercial organisations to provide support services such as payroll and IT services, this gives private sector an in-built advantage in the commissioning support process, claimed the BMA.
The Department of Health's draft guidance, Developing commissioning support: Towards service excellence, has made recommendations on how a CCG's technical and back-office functions should be provided from 2013.
Concerns that proposals could lead to an imbalance of power between clinical commissioners and large, commercial providers of support, could serve to undermine the goal for clinician-led and locally-focused commissioning.
"The government promised a greater role for clinicians in its plans to reform the NHS and created CCGs, placing local GPs and other healthcare professionals in a leading position in the commissioning process," said Dr Laurence Buckman, Chairman of the BMA's GP committee.
"Yet now it seems barriers are being put in place that would undermine the ability of clinicians to take local decisions.
"This latest guidance gives the commercial sector an in-built advantage and appears to be yet another worrying step towards an NHS focused on commercial priorities.
"CCGs need proper professional support, but they must have the flexibility to decide who is best able to provide these services.
"The skills and experience of staff in current PCT clusters will be invaluable as they support the development of CCGs. To provide continuity at a time of huge financial pressure and structural overhaul, current PCT clusters should be supported to become viable commissioning support organisations and should not be forced into an unfair competitive process with large, commercial organisations."