And with climate change likely to raise the risk of flooding through rising sea levels and more rainstorms, £20 billion needs to be invested in flood defences to protect properties in the next 25 years, the agency said.
Some 5.2 million properties are already at risk of flooding, with 2.4 million threatened by rivers and the sea, and a further 2.8 million at risk from surface water flooding from overflowing drains.
Thousands of health centres and doctors' surgeries, schools and miles of railways and roads are also at risk, according to the agency's Flooding In England report.
Almost half a million homes, offices, factories and warehouses are at a significant risk of flooding from rivers or sea - which means they have a greater than one in 75 chance of being flooded in any year.
The highest number of properties at significant risk are in the South East of England, where some 111,356 are threatened with flooding.
Boston, Lincolnshire, has the greatest number of properties at high risk - 23,700 - of any local authority.
According to the latest analysis of the impacts of climate change on the UK released this week, the risk of flooding is set to increase due to rising sea levels, more rapid coastal erosion and increasingly severe and frequent rainstorms.
Without an increase in investment in flood defences an extra 350,000 properties, including 280,000 more homes, will face a significant risk of flooding by 2035, bringing the total to 840,000 under threat, the EA said.
Funding for maintaining and constructing defences will need to double from £570 million in 2010/11 to more than £1 billion in 2035 to safeguard the same number of properties as are currently protected, the Environment Agency said.
Some £150 million a year will be needed just to address the risk of surface water flooding, which caused some of the problems in the devastating 2007 floods, the agency said.
In the floods two years ago, which hit parts of Yorkshire, the Midlands and the South West of England, 13 people died as well as two premature twins, while 55,000 properties were flooded and thousands had to be rescued from the flood waters.
Without increasing funding for defences, the annual cost of damage to residential and commercial properties could rise from £2.5 billion to £4 billion, the agency warned as it released its long-term investment strategy for England.
The Environment Agency's chairman Lord Chris Smith said: "The latest climate change data shows that the risk of flooding and coastal erosion will continue to increase in the future due to rising sea levels and more frequent and heavy storms.
"There are important decisions for us all to take about how to manage these risks to protect people, communities, businesses and the economy in future.
"The Environment Agency has completed 90 flood defence schemes in the past two years, providing increased protection to over 58,000 properties.
"While continued investment in managing these risks is crucial, we cannot always prevent flooding so communities need to take responsibility for being prepared - for example by signing up to the Environment Agency's free flood warning service."
The Environment Agency said more than 430,000 people in flood risk areas had signed up to its free warning service, which provides alerts by text message, telephone or email, and urged those who have not subscribed to join.
Environment Secretary Hilary Benn said: "We have invested record levels of funding in recent years but, as the UK Climate Projections we published yesterday make clear, climate change means all of us will need to do much more in the future to adapt and manage the risks of flooding and erosion.
"We need to make sure that we're up to that challenge - the floods of summer 2007 were devastating for so many people and we all need to work together to make sure we're as prepared as we can be in future.
"That's why I'm calling for a national debate on how we meet the challenge, what our priorities should be and, importantly, how the costs should be met."
Shadow environment secretary Nick Herbert said: "The Environment Agency's call for more investment in flood defence brings home the reality of climate change, and there will need to be a debate on the priorities, but the public must be protected.
"When a staggering one in six homes in England are at risk, it is essential that flood defence schemes are cost-effective and delivered on time, and that no unnecessary development takes place in areas that are susceptible to flooding."
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