Matt Hancock has announced that Public Health England (PHE) is being replaced by a new public body that will be responsible for dealing with pandemics.
The National Institute for Health Protection (NIHP), will also work against the threats of biological weapons and infectious diseases.
“To give ourselves the best chance of beating this virus and spotting and tackling other external health threats now and in the future, we need to bring together the science and the skill into one coherent whole,” he said.
He added: “It will report directly to ministers and support the clinical leadership of the chief medical officers. It will be dedicated to the investigation and prevention of infectious diseases and external health threats.”
The health secretary also announced that from today, Public Health England (PHE),alongside the Joint Biosecurity Centre (JBC) and NHS test and trace will operate under a single leadership, reporting to the Conservative peer Dido Harding.
Baroness Harding is currently in charge of Whitehall's contact-tracing operation.
Hancock said the pandemic had shone a light on the public health system and that he has learned a lot about what needs to change.
The government adopted a new way of counting daily deaths from COVID-19, after concerns were raised that the method used by PHE officials overstated them.
According to the latest government statistics, 41,369 people have died across the UK with coronavirus, and the Office for National Statistics found England had the highest excess death rate in Europe over the first half of 2020.
The new health protection agency for England will be modelled on Germany's Robert Koch Institute which combats infectious diseases.
Expertise from Public Health England and the Test and Trace network will be used to form an organisation focused on tackling the coronavirus threat and future pandemics.
Hancock said he would consult on how the improvement of public health could be embedded in the health system.
“We will use this moment to consult widely on how we can embed health improvement more deeply across the board and I’ll be saying more on this over the coming weeks.
“This will in turn allow the National Institute for Health Protection to focus, focus, focus on the science and the scale needed for pandemic response.”
PHE was formed in 2013 as part of Government health reforms to bring together public health specialists from more than 70 organisations into a single public health service.
The agency supported local authorities and the NHS to plan and provide health and social care services such as immunisation and screening programmes, and to develop the public health system and its specialist workforce, among other responsibilities.