Britain may have to choose whether it wants to save "town or country" from future flooding because it is too costly to defend both, the chairman of the Environment Agency said.
Lord Smith said "difficult choices" would have to be made over what to protect because "there is no bottomless purse" to pay for defences.
His warning comes as it emerged victims of the flooding are having to pay up to 41p a minute to call a government helpline for advice.
The Sun said all money from the 0845 premium-rate number, which was set up by the Environment Agency (EA), went to a private firm.
However David Cameron has now said he wants the a premium-rate helpline to be "scrapped as quickly as it possibly can be", according to his official spokesman said.
Meanwhile householders have been told to brace themselves as further wind and rain threatens to bring more chaos to waterlogged communities across Britain.
Around 180 homes were flooded during during a busy weekend for the emergency services and EA workers up and down the country.
But as flood-hit communities enjoyed a break in the bad weather yesterday, forecasters warned there may be worse to come.
Writing in the Daily Telegraph, Lord Smith defended the EA after a week in which it has come in for heavy criticism over its handling of the crisis, which has left large swathes of the Somerset Levels underwater for more than a month.
He said that the sea surge in December reached higher levels than the east coast surge of 1953, which cost more than 300 lives, but without the loss of life because of advances in flood warning and risk-management.
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But he said that "there are no quick fixes in the face of this kind of extreme rainfall", and tough decisions lie ahead, not just for the EA, about how protection from flooding is managed in the future.
Lord Smith said: "Yes, agricultural land matters and we do whatever we can with what we have to make sure it is protected. Rules from successive governments give the highest priority to lives and homes; and I think most people would agree that this is the right approach.
"But this involves tricky issues of policy and priority; town or country, front rooms or farmland?
"Flood defences cost money; and how much should the taxpayer be prepared to spend on different places, communities and livelihoods - in Somerset, Lincolnshire, Yorkshire, or East Anglia? There's no bottomless purse, and we need to make difficult but sensible choices about where and what we try to protect."
Following a meeting of the Government's Cobra emergencies committee yesterday, Environment Secretary Owen Paterson said that 73,000 homes in England had been protected from flooding since Friday, and that the EA continued to protect communities by deploying demountable flood defences, sandbags and clearing waterways.
He said: "I have enormous sympathy for those who have been affected again this weekend and the government is working with all local councils to help communities recover. All requests for assistance have been met."
News that the EA's Floodline phone number costs 10.5p a minute from landlines and 41p from mobiles was met with fury by residents in flood-stricken communities, The Sun said.
Bryony Sadler, a member of Somerset's Flooding on the Levels Action Group, told the newspaper: "We are extremely grateful to the Environment Agency's people on the ground, who are doing their best to help us.
"But this is just another example of staggering mismanagement form their pen-pushing bosses."
Residents in Somerset were also left on edge following the discovery by a microbiologist that flood waters contained more than 60 times the safe level of bacteria.
EA staff have been working around the clock to alleviate the flooding hell that people in the county have endured for five weeks, pumping 1.5 million tonnes of water a day off the Levels.
Two specialist all-terrain vehicles have been sent to the county along with extra pumping equipment.
But with further rain expected following the wettest January on record in some places, saturated ground and high river levels could lead to further river flooding this week.
Weather forecasters are expecting winds of up to 70mph today, and up to 30mm (1.2in) of rain.
Officials say fresh flooding could affect the south coasts of Devon and Cornwall today as well as Somerset, Dorset, Hampshire and the Isle of Wight.