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Parts of the area being earmarked for a huge ‘garden city’ at Ebbsfleet and Dartford could be prone to severe flooding.
The Environment Agency flagged up the threat in a report four years ago, in which it set out the potential risks of flooding across north Kent, along with ways in which it could be managed.
In the report, Ebbsfleet and Dartford were identified as areas with one of the highest concentration of properties at risk within the wider north Kent area.
It said 1,282 homes could be at risk during a “once in a century” event.
Under a section headed “Key Messages” the report stated: “Flood risk in areas to be developed needs to be well understood so that proposed developments do not people at risk.
“The sub-area covers the lower reaches of the River Cray from Crayford down to where the river joins both the Crayford and Dartford Creeks which converge with the Thames estuary.
"The tidal flooding consequences are extremely severe and therefore a high level standard of protection exists to protect Dartford town from a 0.1% event.”
Meanwhile, the leader of the Local Government Association has warned government plans to set up an urban development corporation to oversee the development could shut out the views of councils.
LGA Conservative chairman Sir Merrick Cockell said: “While we support the government’s aims to build more houses, democratically-accountable councils have been at the forefront of delivering local growth and the creation of a separate, remote quango is unnecessary.”
He added: “Residents will be concerned that such a body, unelected and accountable to central government, could have the power to make local decisions about investment, planning, development and possibly even local transport.”
He also queried whether the areas affected would get any of the financial benefit.
Meanwhile, the Kent branch of the CPRE (Council for the Protection of Rural England) gave a cautious welcome to the scheme.
“Flood risk in areas to be developed needs to be well understood so that proposed developments do not people at risk" - Environment Agency report
Richard Knox-Johnston, vice president of CPRE Protect Kent said “CPRE has been campaigning for action to unlock sites with planning permission, especially those, such as Ebbsfleet, where the land is designated “brownfield”.
"We look forward to seeing Government finding a solution to unlock this land.”
The Chancellor George Osborne will set out further details of the scheme when he delivers his budget statement.