Speaking to delegates at the NHS Confederation conference, Ms Flint said the NHS needed to move public health 'beyond balloons and baseball caps' and 'really get down to the money'.
'We are facing today and will do so in the future a time-bomb of ill health caused by activities that can be moderated,' she added.
Ms Flint said NHS managers needed to make sure the staff they were asking to implement health inequalities targets actually understood what was expected of them.
'We need to make sure that what the target is is not lost in translation,' she said.
'The task now for primary care trusts.and providers is to demonstrate accountability on the ground,' she added.
Department of Health director of public health at the Dr Valerie Day said the NHS needed to be much cleverer at relating what was spent with what was needed.
'There is no correlation between the money being spent on cancer treatment for example and the need for it,' she said.