Officials at the agency - Sepa -warn the risks are likely to increase as global warming triggers heavier rain, fiercer storms and higher sea levels. The Met Office already predicts 2014 will be one of the world's warmest-ever years.
Sepa's maps show the areas of Scotland most at risk from flooding by rivers and sea. They are due to be publicised and augmented this week, highlighting specific hazards for people, property and public services.
Scotland and the rest of the UK suffer a sustained battering from a series of storms, strong winds and high tides over Christmas and new year. Last month was Scotland's wettest December since records began in 1910, and saw the lowest bad-weather pressure system in the UK since 1884.
Sepa's maps show four of Scotland major airports are on low-lying land next to rivers or estuaries likely to overflow. Much of Edinburgh, Dundee and Inverness airports could be submerged, while the edges of Glasgow airport are under threat.
Two coastal power stations on the Firth of Forth - Longannet in Fife and Cockenzie in East Lothian - are at risk from storm surges and high tides. Sections of the M8, M9, M90 and A9 are vulnerable, as are parts of the Edinburgh-Glasgow rail line.
Other vital facilities under threat are the Faslane nuclear submarine base on the Clyde, the Rosyth naval base on the Forth, the vast petrochemical complex at Grangemouth, Edinburgh Royal Infirmary, Seafield sewage works in Leith and Saughton prison in Edinburgh.
The online maps show the Scottish Government's grand headquarters at Victoria Quay on the Edinburgh shoreline to be surrounded by threats from the Forth and the Water of Leith.
Dr Richard Dixon, director of Friends of the Earth Scotland, said: "The prospect of nuclear missiles inundated by flooding seawater is particularly appalling."
The public had to be reassured that key facilities were protected, he argued. "With the risk of major flooding increasing every year we need to know that no-one is going to be caught napping," he said.
Dixon says "climate chaos" is being driven by carbon pollution from human activities, making the weather less predictable and more extreme.
Along with the risks to crucial infrastructure, Sepa has previously said there are 243 areas of Scotland vulnerable to flooding, including many in the central belt. Over 125,000 properties, one in 22 homes and one in 13 businesses, are reckoned to be at risk from flooding.
"There is a consensus among leading climate scientists that we will continue to see increasing temperatures, accompanied by increased rainfall, stormier weather and a general rise in sea level," said Sepa's head of hydrology, Richard Brown.
"The frequent and severe weather we have experienced over recent years in Scotland and across the rest of the UK may be a taste of what's to come, which is why Sepa is supporting Scotland's plans to prepare for such eventualities."
Along with other agencies, Sepa is preparing strategies to make Scotland more resilient to cope with climate change, Brown told the Sunday Herald. "The publication of the new flood maps on January 15 is a major milestone in preparing these strategies."
Sepa said the new maps would build on current ones to show the risks to people, property, community services and other important sites. They will include flood depth and velocity in areas at greatest risk.
The Scottish Government stressed a direct link could not be made between recent storms and global climate change. "But spells of severe weather in the middle latitudes are entirely consistent with what we expect in a warming world," said a spokesman.
Evidence from the United Nations suggested severe weather events could get more frequent as a result of climate change, he said, adding: "Most of the weather we saw was in line with normal winter expectation although it was unusual to see front after front without sustained break.
"The Scottish Government is showing leadership and building on progress already made to increase the resilience to the impacts of climate change by developing Scotland's first climate-change adaptation programme."
The Government's Edinburgh headquarters would be protected, the spokesman added.
The Met Office said that this year will be one of the 10 warmest worldwide since records began in 1880. The 10 years with the highest global average temperatures have all been since 1998, with the hottest in 2010 and 2013 currently ninth warmest.
Scientists said rising temperatures are likely to bring more wild weather. A report by the European Academies Science Advisory Council said Europe has suffered a 60% increase in extreme weather events recorded by the insurance industry since 1980. There has been a fivefold increase in the major floods previously expected only once in 100 years.