Britain is dangerously unprepared for a flu pandemic that could kill as many as 315,000 people, mainly because of changes the coalition has made to the NHS, a report claims.

The NHS would struggle to cope with a catastrophic outbreak of flu, with its response seriously hampered by a host of problems related to the radical restructuring of the NHS in England, according to the Centre for Health and the Public Interest (CHPI), a health thinktank.

The government's own national risk register of civil emergencies, which details any "event or situation which threatens serious damage to human welfare in the UK", identifies pandemic influenza as one of the four highest priority risks" the country should prepare for, alongside major terrorist attacks, coastal flooding and volcanic eruptions abroad.

The Cabinet Office has advised local resilience forums to lay plans to tackle a potential pandemic that could affect up to half the population, lead to as many as 4% of those affected being admitted to hospital, and cause "excess deaths in the range of 210,000-315,000 nationally".

The CHPI's assessment of the UK's preparedness to deal with pandemic flu states: "The NHS is already struggling to deliver on the 'day job' of routine emergency admissions, so would be exceptionally challenged by a crisis such as a flu pandemic."

The response to a future mass outbreak of flu is likely to be less coherent and effective than the response to the arrival of swine flu in 2009, which claimed 457 lives and was widely regarded as a model of good planning and successful intervention.

The CHPI report says the controversial shake-up of the NHS in April – which saw scores of existing organisations replaced with several hundred new ones – has caused problems across the board.

"There appear to be new difficulties from top to bottom, from central policy-making, through loss of expertise resulting from the substantial staffing and organisational changes caused by the re-organisation, down to the ability to deliver at a local level. There are too many new problems for comfort," conclude Dr Hilary Pickles, a former director of public health who has also worked for the Department of Health (DH), and David Rowland, a health and social care policy researcher.

The emergency response could be weakened by confusion over the roles and responsibilities of the large number of organisations responsible for different areas of NHS care and health policy – the Department of Health, NHS England, Public Health England and the chief medical officer – leading to "a lack of clarity … about who does what", the report warns.

It also casts doubt on whether the emergency powers the health secretary can exercise over the NHS in the advent of a pandemic will ensure that all NHS organisations, including hospitals, would do what would be needed.

The authors also raise questions about the ability of the NHS's 111 telephone advice, out-of-hours care services and GP-led clinical commissioning groups to help relieve a crisis that could affect 30 million. NHS England's role may also be hindered by having many fewer staff than its predecessor bodies, they say.

Dr Maureen Baker, chair of the Royal College of GPs and a leading authority on flu, said the report bore out the college's warnings about the shake-up's impact on the NHS's ability to cope with pandemics.

"We agree with the analysis in this report and share similar concerns about where the responsibility, accountability, and decision-making sits, particularly at a national level," she said.

"Establishing vaccination systems and anti-viral distribution is something that needs to be planned centrally and with the current NHS structure, it's not apparent how this could work effectively in a pandemic situation."

Richard Coker, professor of public health at the London School of Hygiene and Tropical Medicine, said the report shows that, if a flu pandemic struck, "the NHS is likely to be found wanting and current reforms hinder rather than help in facilitating a cohesive national response."

The DH said: "It is wrong to suggest that the new health system will not be able to cope with a flu pandemic. A great deal of work has been carried out by the Department of Health, Public Health England, the NHS and local authorities to make sure national and local plans are up to date and fit for purpose."