The institute has said indicators will now be based on its quality standards under plans set out by the DoH in its response to the White Paper Liberating the NHS.
Stakeholders will be able to influence the design of quality standards, but not directly put forward new QOF indicators.
Experts warned the changes may marginalise orphan conditions and exclude public and charity participation.
In disease areas where no quality standards yet exist, only NHS Evidence-accredited sources will be used to formulate new indicators. This appears to rule out stakeholder input altogether until later consultation. NICE plans to write 150 standards in total, but just 12 are finished with 16 more in development.
GPC deputy chairman Dr Richard Vautrey said: 'Contributing ideas for QOF should remain as open as possible and I would be extremely concerned if the processes that NICE was putting in place made this more difficult.'
Former GP Dr Chris Manning, founder of the Primary Care Mental Health and Education group, warned that the voice of the public and smaller charities for orphan diseases could be lost in the 'endlessly convoluted' process.
Louise Lakey, policy manager at the Alzheimer's Society, welcomed integration of dementia quality standards into the QOF but added: 'The challenge is to ensure that people have a voice and that the framework is able to respond to the changing environment and emerging medical advances.'
A NICE spokeswoman pointed out that its quality standards were subject to public consultation.