Experts raised concerns about the transition to the new system in a meeting of the Joint Committee on Vaccination and Immunisation (JCVI) in February.
Advisers said local public health directors may lack the powers to influence public health measures, while systems that monitor childhood vaccination uptake may be disrupted.
It comes after public health leaders said the NHS reforms have left emergency plans ‘confused’, posing a ‘real risk’ that no-one will take command in a future public health emergency.
The minutes, published last week, show that advisers warned about a lack of clarity on who would have responsibility for managing the data that allows ministers to appraise immunisation coverage.
Members added that it was unclear how directors of public health in local authorities would be able to identify potential problems and rapidly change local provision to overcome issues in immunisation programmes.
They warned: 'Under proposed arrangements, directors of public health appear to lack robust levers to influence public health measures.'
Experts said there may be a shortage of qualified directors for the roles, and that it remained 'unclear how schools-based programmes would be resourced and supported'.
The committee urged that 'it is vital that the success of the immunisation programme be maintained and protected'.
A recent report led by former CMO for England Sir Liam Donaldson criticised the coalition's response to swine flu in the year after the pandemic. His review found the scrapping of a flu awareness campaign may have cost hundreds of lives.
Under the government's reforms, Public Health England (PHE) will replace the Health Protection Agency and similar bodies from April 2013.
In future, immunisation programmes will be commissioned by the NHS Commissioning Board to a plan developed by PHE.