Professor Alan Maryon-Davis, honorary professor of public health at King's College London, said the idea could strip funds from consortia that cover deprived areas.
These areas tend to have poorer health, making commissioning more challenging.
Speaking at a Westminster Health Forum health inequalities conference in London last week, Professor Maryon-Davis said: 'My anxiety is that the health premium could be distorting: those who make no progress may miss out on the health premium and might fall further behind.'
The quality premium, outlined in the Health and Social Care Bill, will reward consortia which display successful commissioning.
Success will be judged on financial management and outcomes for patients, although the details of precisely how this will work are yet to be revealed.
Payments are likely to be taken from existing GP funding. They will be distributed among practices and could comprise up to 15% of GP income.
GP leaders have expressed concerns over the impact of the premium. BMA chairman Dr Hamish Meldrum said there was a 'genuine and legitimate fear' the premium may lead patients to accuse GPs of making decisions for 'financial rather than clinical reasons'