It said plans for a 'health premium' could disadvantage areas with the hardest task.
The comments echo those of Professor Alan Maryon-Davis, honorary professor of public health at King's College London, who said the move could strip funds from consortia in deprived areas.
In its response to the White Paper Healthy People, Healthy Lives, the NHS Confederation backed plans to prioritise public health and said it provided 'a major opportunity'.
But funding arrangements were a concern, it said. The proposed health premium, separate from the 'quality premium' that consortia are likely to receive based on patient outcomes and financial management, would reward areas that reduce health inequalities.
However, the NHS Confederation fears it 'may not fairly reward progress and may lead to areas losing money where there is actually most need'.
Areas with high population movement, often deprived areas, find it more difficult to track improvements - a further disadvantage. Even those which cut health inequalities may be inadvertently penalised by a reduction in their deprivation indicators, it added.
NHS Confederation deputy policy director Jo Webber said: 'The approach to the health premium is in urgent need of review because, as it currently stands, the incentives to address long-term health challenges in the most deprived areas will not be there. A key government objective in reducing health inequalities will be put at risk.'
Ms Webber also warned that it was important to ensure GP consortia have access to public health expertise to ensure services are commissioned using evidence and cost-effective policies.
The NHS Confederation also warned that local authorities may not have enough money to commission and deliver all public health services.