The Gateway, which is to be the site of up to 120,000 new homes, is a former marshland that is vulnerable to regular inundation.
The Environment Agency and independent experts have proposed a "green grid" system. This groups housing around parks and woodland, which will act as sponges in the event of a flood.
The plans for the grid system were discussed in a meeting at the Greater London Assembly on Tuesday. The meeting was attended by representatives from Thames Water, the Association of British Insurers and the London Development Agency.
Samantha Heath, the chair of the GLA's environment committee, said at the meeting that the government had budgeted £500m for a viable system of flood prevention.
London mayor Ken Livingstone backed the idea of a network of linked open spaces in the Thames Gateway in October last year.
Roger Leveret, a sustainability consultant, voiced concerns about the suitability of the area for intensive housing development.
He said: "We are sleepwalking into a chain of problems. The location is vulnerable to flooding and better solutions to the housing problem, such as densification of housing in existing areas, are being ignored."
Michael Owens, the head of partnership development at the London Development Agency, estimated that flood prevention would cost about £2500 a house, assuming that 60,000-90,000 homes are eventually built.
This figure is in addition to the money already spent on London's sea defences, such as the Thames Barrier. It is expected that rising sea levels and severe weather caused by global warming will make existing flood defences obsolete by 2030.
A team of 15 has been set up by the Environment Agency and the Thames, Anglian and Southern water companies to plans measures to protect settlements along the 212 miles of the Thames.