The UK has stockpiled millions of doses of tamiflu
A flu pandemic is the gravest threat to UK security as it could claim up to 750,000 lives, according to a new National Risk Register.
The document, published for the first time, weighs up the likelihood of threats and their potential impact.
The most likely threats are attacks on the transport network and on computer and communications systems.
Britain has stockpiled enough doses of the antiviral drug Tamiflu to treat 25% of the population, the document says.
The risk register, which had been kept secret until now and will be updated annually by the Cabinet Office, sets out the various dangers faced by the UK and how they are viewed by government advisors.
BBC security correspondent Frank Gardner said that while officials insisted the register was not intended to rank dangers in any kind of priority, it was clear that pandemic flu had emerged as the gravest threat to national security.
While a flu pandemic is not as likely as a terrorist attack, its potential impact is much wider, as it could infect up to half of the UK's population, it says.
The government predicts, based on "historical information, scientific evidence and modelling", that between 50,000 and 750,000 people could die.
The Spanish Flu outbreak of 1918 -19 is estimated to have caused 20 to 40 million deaths worldwide - 228,000 of which were in the UK.
The report says another pandemic on a similar scale would also have social and economic consequences - impacting on essential services, creating shortages and distribution difficulties.
"Experts agree that there is a high probability of another influenza pandemic occurring but it is impossible to forecast its exact timing or the precise nature of its impact," the report says.
But it said the government had stockpiled enough oseltamivir - the antiviral drug known as Tamiflu - to treat 25% of the population which "should be sufficient to treat all those who fall ill in a pandemic of similar proportions to those that occurred in the 20th Century".
An illustration of the major risks in the report suggests that electronic attacks on computer or communication systems and terrorist attacks are among the most likely threats, but would not have the widespread impact of a flu pandemic.
And while flooding is deemed less likely, its potential impact is predicted to be wider.
Ian Kearns, of think tank IPPR's security commission, said the register was aimed at encouraging public and private organisations to think about their response to major emergencies.
"You might want to ask the question, for example, what happens if many of our heavy goods vehicle drivers fell victim to that influenza and weren't able to perform their jobs?
"Do we have enough back-up to be able, for example, to deliver food to the supermarkets?" he said on BBC Radio 4's Today programme.
Security Minister Lord West rejected suggestions that the publication of the register might cause unnecessary alarm and said he hoped people would be reassured by the amount of work done.
"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 the BBC.
For the Conservatives, Baroness Neville-Jones welcomed the register but said Britain compared "extremely poorly" with comparable countries on stockpiling oil and gas resources for an emergency.
She said the Conservatives would set out their own national security green paper in the next few months.