Previously secret information ranked a terror attack on transport as the most likely risk faced by the country, raising the spectre of another 7/7.
The second most likely form of threat is an electronic attack on IT and communications systems, and the third most likely is a terror strike on a crowded place.
The complex analysis in the Cabinet Office's National Risk Register looked at a wide range of threats to the country, including natural disasters and industrial accidents.
Different threats are ranked on a specially-devised graph according to "relative likelihood" and "relative impact".
The document said: "Of the different malicious attacks outlined in this document, conventional attacks on transport systems are judged to be some of the more likely to occur.
"This assessment is supported by the many examples of this type of attack perpetrated by different groups across the globe."
Railways, including underground train systems in UK cities, are "more vulnerable to attack" than airlines because of different security levels, it said.
As announced by Prime Minister Gordon Brown in March, the document said a flu pandemic was the biggest threat facing the country.
Such an incident would be the most damaging, claiming up to 750,000 lives.
But it is only the fifth most likely type of risk, according to the new information, and is ranked as slightly less likely than a severe weather attack.
Coastal flooding was given as the second most damaging type of threat.
The document also provided advice to families and organisations on what they can do to protect themselves.
It built on information contained in the Preparing For Emergencies booklet which was delivered to every household in the country in 2004.
Today's new information ranked a chemical, biological, radiological or nuclear (CBRN) attack by terrorists as about as likely as a major incident of inland flooding.
"The use of some CBRN materials has the potential to have very serious and widespread consequences," it said.
"An example would be the use if a nuclear device.
"There is no historical precedent for this type of terrorist attack."
The document said the Government has stockpiled enough doses of the antiviral drug oseltamivir, known as Tamiflu, to treat a quarter of the population.
"This should be sufficient to treat all those who fall ill in a pandemic of similar proportions to those that occurred in the 20th century," it said.
"The Government is collaborating actively with international partners on prevention, detection and research, and is taking every practical step to ensure that the UK is prepared to limit the internal spread of a pandemic and to minimise health, economic and social harm as far as possible."
Security Minister Lord West of Spithead rejected suggestions that publication of the register would simply cause unnecessary alarm.
"I have great faith in the public and they would prefer to have information because the thing that causes fear is ignorance of things," he told BBC Radio 4's The World at One.
"A thing like the flu pandemic, it's very difficult to gauge exactly what the scale of it will be.
"We have done a great deal of work on it and I hope when people read this they will be reassured by the amount of work that we have done within government."
Shadow security minister Baroness Pauline Neville-Jones said: "We welcome the publication of this register.
"We have been urging the Government to be more open about the risks the UK faces for some time.
"However the real value of it will depend on how good the information supporting it is and if the Government actually deals with the threats it highlights.
"For example, while the resilience of supply chains is crucial we compare extremely poorly with comparable advanced economies when it comes to stockpiling oil and gas resources to sustain us through an emergency.
"On cyber-crime, a Lords Select Committee has condemned the Government's 'head in the sand' approach."
She added: "In the next few months we will publish a national security Green Paper.
"This Green Paper will set out an effective national security strategy dealing, among other things, with the resilience of the UK to withstand emergencies."
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