A pandemic flu bug would pose a greater threat to Britain than terrorism, according to a register of risks that has been kept secret until today. Deaths from global flu will be on a scale far beyond anything related to such an attack, the Government will say.

Until now, the official list of threats and risks facing Britain has been kept confidential, although MI5 has for some time published on its website the terrorist threat level, currently defined as severe.

Plans to publish a risk register were announced by the Prime Minister in March during a statement to the Commons on national security strategy. Top of the list is pandemic flu because of the conviction in Whitehall that it is “not a question of if but when” and that it could kill 750,000 people.

The Cabinet Office risk-register report does not include a top-ten list of threats as this was deemed unhelpful in trying to inform people of the kind of threats facing Britain.

Instead, the report has a graph with two lines highlighting the “relative impact” and “relative likelihood” of various threats. Pandenic flu is way ahead on potential impact but terrorism is highest in terms of a likely occurrence. The other main risks include climate change, flooding, severe weather and attacks on critical national infrastructure.

In a little-noticed section of a speech on terrorism given in 2006 by Dame Eliza Manningham-Buller, when she was Director-General of MI5, she accepted that climate change potentially posed a greater threat. “It is difficult to argue that there are not worse problems facing us, for example climate change,” she said during a speech at Queen Mary, University of London.

The risk register places the threats in context, spelling out how they are likely to affect people’s way of life.

On terrorism, according to Whitehall sources, the report will focus on the likelihood of attacks on “transport and in crowded places” and will high-light the growth in terrorist activities in Britain in the past four years.

MI5 is tracking some 2,000 individuals regarded as terrorist suspects. The figure was 500 in 2004, rising to 800 by 2005 and 1,600 by the end of 2006. There are known to be 30 plots being investigated by MI5 and the police, and those convicted since 2000 came from the North, the Midlands and the Home Counties as well as London.

However, a flu pandemic still tops the bill in the register of risks because of the greater impact it could have across Britain and the overwhelming damage it would do to the economy because of the huge casualty rate. The assessment is that the number of deaths would be between 50,000 and 750,000, and that more than a million could need hospital care.

Experts cannot predict when it will happen but say when it does it will come in several waves of three to six months over a two-year period. A Ministry of Defence document recently released under the Freedom of Information Act said that a pandemic would generate “unprecedented levels of public fear, stress and panic”.

The Department of Health has purchased 3.3 million doses of vaccine for the H5N1 strain of bird flu that could give a degree of protection. But the Cabinet Office gives warning that no pandemic vaccine will be available until the virus has been identified and that it will take, it is estimated, four to six months for it to be developed and manufactured.

In his statement in March, Gordon Brown also spoke of setting up a forum of experts to advise the Government in the event of a national catastrophe such as pandemic flu. Whitehall sources said that the current plan was to establish an interim forum and chairman so that the process could start as soon as possible.

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