Cuts to public health staff may leave the NHS lacking specialists able to deal with emergencies, such as a future flu pandemic, it said.
The DoH last month responded to the findings of a consultation on the public health White Paper it published in December 2010.
The government responded to numerous concerns raised in the consultation. These included worries over fragmentation of care as control of public health moves to local authorities and concern over the impact this would have on maintaining expertise in the NHS.
But there was little mention of how the proposed health premium, set to reward public health outcomes, could impact health inequalities.
The health premium - separate from the quality premium which will reward successful commissioning groups - came under fire from co-authors of the Marmot Review into public health who met the House of Commons health select committee earlier this year.
The DoH said work was ongoing to improve this part of the reforms, promising updates in the autumn to 'complete the operational design of the public health system'.
The BMA said the government's focus on public health was laudable.
But Dr Keith Reid, co-chairman of the BMA's public health medicine committee, said it was 'disappointing' that concerns remained about how health issues, such as obesity, alcohol misuse and STIs, should best be tackled.
Dr Reid added that the financial climate and NHS restructuring meant posts in public health were being cut.
'We do not want a situation where local authorities are handed the keys to public health, only to find that the engine has gone,' he said.
The BMA wants a commitment from the government to maintain the current level of public health specialist posts.