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.
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.
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.
As of this morning the EA had three severe flood warnings in place, one covering large parts of Cornwall and Devon, and two for the River Severn in the Midlands. There are also 95 flood warnings and 233 less severe flood alerts.
The River Severn in Shropshire, Telford and Wrekin, Worcestershire and Gloucestershire, the Frome and Avon in Dorset, the river Thames and its tributaries in Oxfordshire, West Berkshire, Reading, Slough and Hampshire and the Medway in Kent are all of concern this week.
The agency's flood risk manager, Kate Marks, said that as high tides and large waves threaten the south coast, further rain on already saturated ground could lead to river flooding.
She said: "With further severe weather conditions expected in the coming days, the Environment Agency is likely to issue further warnings so people should check their flood risk and get early warnings so they can take action to protect their property."
Meanwhile, the atrocious weather has taken a human toll.
A 67-year-old woman died after being swept out to sea near the mouth of the River Arun at Littlehampton Pier, West Sussex on Saturday.
She was pulled from the water by a lifeboat crew after being carried out to sea by strong currents, but died later in hospital.
In Wales more than 50 mountain rescuers had to battle atrocious weather conditions on Saturday to rescue a group of students who got lost attempting to tackle the 752m Pumlumon mountain in the Cambrian Mountains.
In Newgale, west Wales, 10 people had to be plucked from a bus in the dark after it got stuck on the seafront.
Coastguards said the vehicle was hit by a large wave before being surrounded by flood water.
Six French fishermen off the coast of Cornwall also managed a lucky escape after their boat was hit by a giant wave. Five were winched to safety by helicopter, while a sixth was rescued by lifeboat.
And in Scotland fears are growing for an angler who went missing on the Aberdeenshire coast in the early hours of yesterday morning.
The man was night fishing at Tangle-Ha, north of St Cyrus, when he disappeared from rocks in what were described as "exceedingly rough" conditions.
However, nature's frightening power did not deter a group of 30 daredevils who rode the waves of the "five-star" tidal surge the Severn Bore yesterday.
People took to the water in canoes and on surfboards, despite official warnings to stay away.