The summer floods caused £3bn damage to 55,000 homes and businesses. Chief Executive Barbara Young said "What we saw during the summer was unprecedented rainfall - the wettest May to July period in 250 years - and the highest river levels in some places for 60 years."
The report makes 33 recommendations, but singles out the need to decide who is responsible for ground water, which caused two-thirds of the damage over the summer, and to protect crtitical infrastructure. Amendments to the climate change bill were cited as ways to secure critical infrastructure in law.
Chairman Sir John Harman said the Environment Agency needed the help of the Government to make changes in how flood risk was managed.
"Two-thirds of the properties flooded during summer were damaged because drains and sewers were overwhelmed, and there is complexity of who is responsible for surface water flooding. We need a clear coordinating framework to deal with flood risk from drains and sewers, which could see the Environment Agency take on a strategic overview role in England, and the different organisations involved in surface water flooding - such as local government, water companies and Highways Agency - working together at a local level.
"We also need to be assured that the providers of critical public services are taking seriously their role in reducing the consequences of flooding. The extreme flooding showed just how poorly protected much of our vital public infrastructure is - and water and electricity supplies were particularly vulnerable. Regulators need to ensure operators protect critical infrastructure from floods.
"Incident response plans need to consider the possible impact on critical infrastructure more effectively, especially under the threat of climate change," he said.
The report pre-empted many of the suggestions of the Association of British Insurers earlier in the week. Young said that the consequences of the floods will be felt by many over Christmas.
"Many thousands of people had their lives and livelihoods devastated by the events and are still having to cope with the traumatic consequences. Every flood provides a learning opportunity to examine the causes and identify areas for improvement, and the summer floods brought into sharper focus a number of issues - many of which we were already tackling.
"Three of the most important challenges are getting clarity on who does what to reduce risks from urban surface water flooding, protecting critical infrastructure, and securing a long term investment strategy in the face of climate change."
She added that the recent threat of a storm surge was dealt with effectively by the Environment Agency, and that this and the summer floods showed that flood defences were generally in good working order.