The analysis published its previously secret "national risk register" which sets out the most significant threats to the country over the next five years.
A flu pandemic is deemed to be likely to impact on the greatest number of people, with half the population likely to become infected and leaving between 50,000 and 750,000 dead.
But attacks on public transport, at a time the UK's terror threat status is "severe", are judged more likely, in the wake of the 7 July attacks in London in 2005 and those in Moscow and Madrid in 2004.
This is due to the combination of the large number of passengers and the "open" nature of train and underground rail networks, contrasting with the high levels of security at airports.
"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; although the likelihood of them affecting any one individual is still very low," The Scotsman quoted the report, as stating.
An attempt to cause chaos with a computer virus is regarded as the second most likely threat to the country.
The document compares 12 major risks in terms of their potential impact and likelihood of them happening. Attacks on crowded places and severe weather are also more likely than a flu pandemic, though experts believe there is a "high probability" of this occurring.
Other concerns include major transport accidents, such as the Kegworth plane crash in 1989 in which 47 passengers died, animal disease, such as foot-and-mouth outbreaks and inland flooding.