Environment Minister Elliot Morley has defended a "nonsensical" system which prevents parts of Lewes getting flood defences.
In a Westminster debate, MP Norman Baker said protecting some parts of the town but neglecting others was "divisive".
He attacked the cell system which means Lewes is divided when funding for defences is allocated.
The rules mean householders and businesses in Malling and Cliffe look certain to have vital new defences.
But Mr Baker said it was now highly unlikely the town centre west, the Talbot Terrace area and North Street would be offered protection - despite the devastation of the autumn 2000 floods.
The town's MP, who is also the Liberal Democrat environment spokesman, warned: "That is very serious. People would once again have the spectre of flooding hanging over them, with no relief in sight.
"People deserve better than that, after the horrors they went through and the promises that they thought the Government had given."
Mr Baker said the whole town should be treated in the same way. He told Mr Morley: "The idea of dealing with flood defences in cells is divisive and nonsensical.
"I hope that the Minister will say that we will move away from the cell culture to a common community defence standard for the town."
Mr Baker also attacked the points system for examining the value of property rather than the level of devastation when flooding occurs.
Mr Morley admitted dividing the town into cells was not ideal. But he said decisions had to be based on getting the best value for taxpayers. Many properties would be protected in Malling Brooks and Cliffe - but not elsewhere.
He said: "It would not make sense to spend million of pounds on a cell if that is far greater than the value of the property within it.
"We have 1.7 million properties at flood risk and we face demand for schemes all over the country, including in the Uck catchment. We have to use resources in the most effective way.
"If we take a one in 100-year flood event, which is the kind of protection level that I want to see, there are about 218 residential properties at risk in Malling Brooks and 166 in Cliffe. There are also commercial properties.
"Town centre west has a score, but one that is low priority. We have two residential properties at risk there in a one in 100-year event.
"In North Street there are no residential properties at risk in a one in 100-year event. In Talbot Terrace there are six. Some schemes may cost millions to defend a tiny number of properties.
"I know that that is not much consolation to the people who live in those areas, but they cannot expect millions of pounds of taxpayers' money for a very poor return on those cells, when that money could go to other schemes."
Mr Morley added the historic walls in Lewes made it difficult to provide defences in some areas.
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