Sir Liam Donaldson's annual report, published this week, also reveals that his recommendation last year that there should be a review of ways to improve public health has not been implemented, even though 'the need for novel strategies has never been higher'.
He says in the report, On the State of Public Health: 'If I see significant evidence of raids on public health monies in the future, I will not hesitate to draw attention to them.'
However, he declined to endorse ringfenced budgets, saying they were 'unfashionable'.
'In this era, the managerial philosophy is it's better to give people flexibility in their budgets,' he said. 'But I don't want to return to the smash and grab raids of the past.'
Association of Directors of Public Health president Dr Tim Crayford said the lack of political appetite for ringfenced initiatives was 'more in the interests of expediency than of securing good public health'.
He said: 'The evidence of recent years is that today's priorities in the NHS invariably trump tomorrow's investment in public health.'
'This is short-sighted, needs to be reversed, and ringfencing would be one way of doing this.'
A central initiative to monitor how Choosing Health funds have been allocated would be one way of identifying commissioners who refuse to invest in public health, he added.
A review of the public health capacity of primary care trusts and strategic health authorities is to be published 'in due course'.
Sir Liam also revealed that a priority for this year would be improving hand hygiene in hospitals.
Alcohol hand rubs will be placed by hospital beds and patients will be encouraged to ask doctors and nurses whether they have cleaned their hands. Pilot studies are to be carried out, although the sites have not yet been finalised.
'I believe that by empowering patients to work with healthcare professionals on this issue we can improve hand-cleaning rates among healthcare staff and reduce the number of infections,' Sir Liam said.
His report also proposed registering everyone as an organ donor unless they opt out; making extra checks on radiotherapy machines; and conducting more research into the deaths of babies during labour.
Steps should also be taken to increase the number of women in senior medical positions, he said.
Of the 23 recommendations he made in last year's report, he rated progress on eight as 'excellent', 11 as having 'met expectations' and four as 'needing further action'.