The Environment Agency is now a statutory consultee for all development applications in areas of England at risk of flooding.
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Agency head of planning Mark Southgate said the new powers came as an unavoidable consequence of climate change.
'Local Planning Authorities must now consult the agency before making any decision on planning applications for developments in areas of greatest flood risk,' he said.
'Planning processes must adapt if we are to encourage new development without placing people and property at risk.'
The new powers are part of the Government's 'Development and flood risk' guidance published in 2001.
It will be clarified by a further statement to be published later this year.
'Planners will also have to consult the agency on all large scale developments - over one hectare - wherever they are located, to ensure that surface water runoff will not cause flooding elsewhere,' said Southgate.
Until now planners had been advised to consult the agency but now the consultation is compulsory.
'We need to make sure homes, particularly for those who are vulnerable, are built in a safe place,' said Southgate.
'This will protect our environment, but also protect people.'
