Climate change experts have angered farmers after questioning whether it was fair to spend £100 million of taxpayers' money to save the Somerset Levels.
Climate expert Lord Krebs has sent a letter to Environment Minister Owen Paterson saying the Levels should not be made a special case and any plan should be good value for money.
Earlier this week the Owen Paterson received an action plan outlining £100 million worth of measures that need to be taken to safeguard the area from future flooding.
The Government has pledged £20 million towards dredging and the clean-up operation, but it is still unclear where the money for major capital projects such as the £30 million barrage on the Parrett will come from.
The Committee on Climate Change warns Mr Paterson that defending the Levels will become "ever more difficult" as sea levels rise by 12cm by 2030 and intense rainfall events become even more common.
Lord Krebs, chairman of the adaptation sub-committee, tells the Minister that the Levels is "a largely engineered wetland landscape" and any public funding should face strict face tests to ensure "value for money is being achieved".
"Funding from central Government for flood risk management is limited, and as a result many worthwhile projects have to held back each year," he said.
"Whilst the immediate needs of the affected communities will be a priority, it would be unfair in the long-term for the Levels to attract more taxpayer support than similar areas elsewhere.
"The long-term approach needs to be sustainable and cost-effective. It shouldn't require taxpayer funding to be diverted from other projects that would deliver greater flood risk benefit."
A report from the committee points out that 900 new houses have been built in Sedgemoor in the ten years to 2011 and says farmers have also contributed to the problems by planting fields with maize.
But farmers say it's easy for Lord Krebs to make judgments from his office in the Horse of Lords or Oxford University, and he should visit the Somerset Levels and see the devastation for himself.
A spokesman for the National Farmers' Union said: "Yes, we do need have to have a debate about climate change in the longer term, but now is not the time to have it.
"At the moment what we are trying to do is dig people out from a terrible mess caused by 20 years of inaction from governments of both stripes. A mess that was not of their making.
"It's all very well for Lord Krebs to dish out advice about sea levels from behind a nice dry desk in a nice warm office but is he really going to tell the poor folk on the Somerset Levels that they should not have taxpayers' money spent on them even though none of this is their fault?"
The NFU spokesman said that if the Government wanted value for money they should have seen that it would have been cheaper to have spent money on flood prevention than pay for an expensive pumping and clean-up operation afterwards.
"In the longer term we have to look at land management practices, but the Government need to understand that there's no point spoiling the plan for an h'apeth of tar and now is not the time to wade in saying people should be left high and dry," he said.
Lord Krebs praises the Somerset Levels and Moors Task Force for recognising that farming practices, soil conservation, peatlands restoration and making properties more resilient should all play a part in protecting the Levels.
But he urged planners to avoid further development in the area until they know that measures such as dredging are working and tells the Government that lessons learned on the Levels could be used elsewhere.
Sharing costs among those who have a role and interest in avoiding future flood damage would bring different interest groups together, he said.
"There's a broader question of which bits of managed landscape do we decide to carry on defending and which bits do we say we have to use as natural soft defences for flooding; they are just there to absorb water, " Lord Krebs told The Times. "I'm not saying people should get out of the Somerset Levels because I think it's too early to make that judgment. But... we must ask ourselves how we prepare the country for flooding which the models suggest will become more common. It may well be the case that there are areas too expensive to defend."
But John Osman, the leader of Somerset County Council, challenged Lord Krebs to "come to Burrowbridge and say that to the people who have been cut off for eight weeks".
Bridgwater MP Ian Liddell-Grainger wants the proposed Parrett barrage funded from general taxation but expects a local flood tax to be considered for other measures.
"Lord Krebs is wrong," he said. "We have to manage climate change, not give in to it. Since 1995 there has been a moratorium on doing anything other than bird sanctuaries and environmental issues."
The Adaptation Sub-Committee (ASC) of the Committee on Climate Change is due to present its first statutory report to Parliament in the summer of 2015.
Responding to the Krebs letter, a Defra spokesperson said: "These proposals were addressed in the Action Plan. The recent weather has had a devastating impact in Somerset. Government is investing £20.5 million to help the community recover and better protect it for the future."