An environmental impact report gave the thumbs down to the pounds 1.5bn Project Moses, which is designed to protect Venice against high tides and rising sea levels.
The committee outlined four main objections: the project did not meet the objective of re-establishing the environmental equilibrium of the lagoon, it failed to integrate with the other initiatives for the protection of Venice and risked damaging them, and it entailed significant damage to the port.
The Venezia Nuova consortium, which has designed and would have built the 100ft-high flood barriers, is now expected to press for the matter to be decided directly by the Italian cabinet, or the Prime Minister.
"The committee's report shows that despite serious pressure and lobbying by Moses backers, it has been able to maintain its independence," said Venetian Senator Giorgio Sarto, a Green and a town planner.
"Those backing Project Moses present it as the only possible solution and invoke apocalyptic scenarios to push it through. Anyone who opposes the floodgates is depicted as wanting to see Venice sink. We face the same problems as our ancestors and like them must find ways that don't damage the ecosystem and don't cost the earth," he said.
The Greens and other environmental groups, such as Italia Nostra or Legambiente, have long argued that a series of integrated "soft" measures could reduce the height of the tide reaching Venice by about eight inches. The basic principles are reducing the flow from the Adriatic into the lagoon, creating more space in the lagoon for the water to expand and lifting Venice up by adding another layer to its foundations.
They advocate the closure of the Canale di Petrolio, the artificial channel in the lagoon that is used by tankers. They say that its depth creates a passage for extra water to arrive in Venice and accentuates the process of erosion.
"Curving the entrance to the lagoon and filling in the holes in the seabed created by erosion is crucial to further reducing the flow of water," said Mr Sarto. "Freeing up the fish farms and other areas currently sealed off within the lagoon will also allow the water to expand once inside."
The strategy involves raising the land level of Venice itself. Recent digging around the Malibran Theatre has revealed visual proof that Venice has been successively raised over the centuries to beat the problem of high tides.
"In the lowest parts of the city we can raise the pavements on average to 1.2m above sea level at the same time as we are doing the maintenance and cleaning work, just as they have done for centuries," said Stefano Boato, a Green member of the Venice Council.
After decades of neglect, several years ago the city administration began a clean-up. Boats with metal arms dredge the canal floors, pulling up rubbish and silt. Forty per cent of the canals have now been cleaned, with 110 thousand cubic metres of silt sucked out.
Raising the "ground level" is underway in three areas of the city. In the Ghetto, a half-mile stretch has been raised by six inches by inserting a layer of stone or sand immediately under the pavement. Residents are offered grants of up to 80 per cent of the cost of raising their foundations to match the newly elevated "footpath".
"These initiatives have already been endorsed in three special laws for Venice since 1973, which provide extraordinary funds for preserving the city. Only a fraction of those provisions have been implemented," Mr Boato said.
The Italian Public Works Ministry first asked for tenders on projects to protect the lagoon city in 1975. As the implications of global warning became clearer, pressure grew for a way to protect La Serenissima from another devastating flood like that of 1966, and from the increasingly frequent high tides.
St Mark's Square and the surrounding tourist shops, restaurants and boutiques stand on one of the lowest lying areas in the city and they can be underwater up to 80 times a year.
The environmental thumbs-down for Moses - despite a favourable opinion by a committee of international experts - is likely to receive a mixed reaction in the city itself.
Massimo Cacciari, the mayor of Venice, who heads a left-wing administration with a smattering of Greens, has been worried that the project would take government funds away from other important city projects. His red- green administration remains divided, mainly opposing the scheme, but with a vocal lobby arguing that it is better to do something than nothing, after so many years of paralysis.