Sarah Lavery, project manager for the team, said: "London is protected up to the year 2030. This study will show what could happen afterwards."
Lavery warned that the maps, which will take five years to produce, will make worrying reading for the government and developers.
She said: "It may not be responsible for the government to let people build over such a huge area."
Lavery said two maps would probably be produced, based on alternative predictions on the effects of global warming.
She said these maps would be similar to those now on the agency's website, which show a scenario with the chance of one flood in every thousand years from 2030.
Lavery said the main difference between the two maps is that the flooded areas in the ones under preperation would not be as deep as those on the 1000-year map.
The maps showing the 1000-year flooding scenario are already causing concerns to developers hoping to build in the Thames Gateway region.
At a Town and Country Planning conference on flooding held last week, Alex Nixon, the sustainability and environmental officer for the Thames Gateway London Partnership, described the maps as a "thorn in the side" of the partnership.
Nixon said: "We believe this could put off investors. Flooding is an emotive issue. If investors see this they may reconsider."