The agency's chief executive Barbara Young said seven of the projects which were approved against EA advice were in areas of the highest flood risk.
These included 10 bungalows, plans for 18 homes and roads and a scheme to convert farmland to a caravan site in areas of Lincolnshire and construction of a new access road in Stowmarket, Suffolk.
Other development proposals were passed despite concerns raised by the Environment Agency over potential risks of flooding by surface water run-off, including an application for 23 houses and 78 flats in Barnet, north London.
The Development and Flood Risk annual report found that decisions were made in line with flood risk advice in 96 per cent of cases where the EA objected and the local authority informed them of the outcome - up from 95 per cent last year.
Since 2001, local planning authorities have increasingly heeded Environment Agency advice and avoided building in areas at high risk of flooding.
But Baroness Young said planning permission was still being granted against flood risk advice and many developers were ignoring the requirement for flood risk assessments to accompany applications.