A report by the Alliance found there is 'an urgent need for frameworks and information' to make clear which aspects of health services, health improvement and health protection GP consortia will be responsible for.
Dr Ken Aswani, lead of the Waltham Forest Federated GP Consortium in London and executive member of the NHS Alliance, said the new health system 'will cause initial confusion' for GP commissioners.
'There is an urgent need for rapid local education over the new structures and how they will work at local level as GP commissioning starts to get real,' he said.
The report, A shared agenda in the new world, warns the pace of the reforms could mean the relationship between the new public health system and GP consortia is overlooked.
It found GPs are already confused by health protection functions, such as vaccinations, and warns the situation will worsen when the Health Protection Agency is merged with Public Health England.
The report was based on discussions with health and public health professionals from across the country.