The decision follows last week's announcement that a new UK Health Security Agency would be established from April, which will focus on responding to external health threats including infectious diseases.
The UK Health Security Agency will bring together the Joint Biosecurity Centre, NHS Test and Trace and some parts of Public Health England, such as the scientific labs and data surveillance teams, that have been responding to the pandemic.
Public Health England's role in health improvement and health promotion will be taken on by the new Office for Health Promotion from later this year. The government said that the new organisation would 'lead national efforts to improve and level up the health of the nation by tackling obesity, improving mental health and promoting physical activity'. It will also be responsible for other public health issues, including sexual health.
Unlike Public Health England, which is an arm's length body, the new organisation will sit within the DHSC. The government said this would enable more 'joined-up, sustained action between national and local government, the NHS and cross-government, where much of the wider determinants of health sit'.
It added that the Office for Health Promotion would help to establish a 'cross-government agenda' and work to implement policy, while a new cross-government ministerial board on prevention will also be set up to drive forward this work.
The head of the new organisation, who has yet to be appointed, will report jointly into health secretary Matt Hancock and England's chief medical officer Professor Chris Whitty.
The BMA said that the cross-government approach 'may signal the type of joined-up working needed to tackle' the drivers of health inequalities.
However Dr Richard Jarvis, co-chair of the BMA Public Health Medicine committee, said there were 'still serious concerns about the centralising of public health within the Department of Health'.
'If we are to address serious public health problems such as obesity and mental health and truly "level up" the nation’s health, we need to see a properly funded and co-ordinated public health system which, crucially, has the organisational independence to speak out when needed to improve and protect the health of the population,' Dr Jarvis said.
Professor Whitty said that the Office for Health Promotion would be critical in helping develop evidence-basad policies that would address the non-direct harms people had experienced from COVID-19.
He said: 'The non-direct harms of COVID on the public’s health will not be trivial. We need an evidence-informed and collaborative approach to health promotion and to support this recovery.
'The Office for Health Promotion will work across both national and local government as well as with the NHS, academia, the third sector, scientists, researchers and industry to develop evidence informed policies.'
Mr Hancock said: 'Good physical and mental health are central to our happiness and well-being. Yet so much of what keeps us healthy happens outside of hospital and the health service.
'By establishing the Office for Health Promotion we will bring health promotion into the heart of government, working to the chief medical office, so we can level up the health of our nation, working across national and local government.
'Prevention is better than cure. By putting in place innovative prevention measures, we can help everyone to live longer, healthier lives as we ease back to normality, and relieve pressures from our NHS.'
The decision to scrap Public Health England was first announced in August last year when the government announced the establishment of the new National Institute for Health Protection. That organisation is now set to become the UK Health Security Agency, which will be led by current England deputy CMO Dr Jenny Harries.