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The Thames Gateway would never be a green role model if an airport wiped out the unique wildlife site at Cliffe Marshes, a Euro MP warned during the conference.
Cliffe has been designated a RAMSAR site of international importance but this has not stopped the Government from including it in options for airport expansion.
Caroline Lucas, Green Party MEP for the South East, urged planners to make the Gateway project a "showcase for the best kind of economy when it comes to housing, low energy and low waste."
But this could not happen if an airport was built at Cliffe. The environmental issue sparked the only verbal fireworks of the conference.
They came after pledges by various speakers to put high environmental standards at the heart of the Gateway project, with plenty of green spaces, low energy consumption and "rainwater harvesting."
Paul Williams, from the office of Deputy Prime Minister John Prescott, said it was important to have an "environmental vision." He said it contained "significant estuarine habitat for over-wintering birds, an area of outstanding natural beauty and Green Belt."
"There is a vision for the major enhancement of the environment for the benefit of existing and new communities," he said. He added that the Gateway project could "accommodate an airport at Cliffe and it could equally well stand without that airport."
Pete Raine, Kent County Council's strategic planning director, said the Thames Gateway should be a national green "role model." But Dr Lucas said that building an airport at Cliffe did not square with the idea of a sustainable economy.
"On the one hand, there is a lot of opportunity, but on the other hand, I am concerned that there will be a temptation to fall back to old-style sites of development," she said.
"More airports and more roads would undermine the very potential of the showcase they think they have in the Thames Gateway."