Chiefs at the Environment Agency (EA) have hit back at what they said was "ill-informed and unfair" criticism of how the quango has handled the flooding crisis.
EA board members suggested that the row was "undermining" public confidence and "belittling" the work of staff working hard to minimise the impact of extreme weather.
It came as communities along the River Thames and in Somerset were warned to expect more flooding into tomorrow as river levels continue to rise, with 16 severe flood warnings along the Thames.
The EA said it acknowledged that a debate about dredging was needed and sympthised with the anger felt by flood victims, but claimed that its work was based on "firm evidence and tested science".
" Of course it is open to anyone to take issue with expert scientific opinion," the agency's independent board members said in a statement.
"But at a time of emergency it is more important for us all to focus relentlessly on managing the current floods and helping to minimise their impact.
"Just as it is wrong to criticise the work of our staff on the ground, it is equally wrong to seek to place blame for the recent flooding events on the chairman and 'people in London'."
The Thames Valley is expected to bear the brunt of the storms this week. Forecasters have said there is little chance of the storms easing until at least next week.
EA chairman Lord Smith said his staff and the Army were helping residents in flood-hit Wraysbury in Berkshire as he issued a fresh defence of how his organisation had responded to the Thames flooding.
He told Channel 4 News: "All the necessary warnings were put in place. We told everyone what was likely to happen.
"Our staff have been out helping in many different parts of the Thames Valley, we were assisting in Datchet last night. I'm told that our staff will be going in, together with the Army to Wraysbury this evening to help there."
Earlier, Communities Secretary Eric Pickles told MPs there was a high risk that the Thames, the Severn and the Wye would all break their banks as water levels rise.
Efforts to deal with the flooding have been overshadowed by a bitter clash between ministers and the EA, after Mr Pickles yesterday issued a barbed apology for relying on its advice.
Environment Secretary Owen Paterson - who was leading the response until being forced to undergo an eye operation - is said to have complained to Downing Street over his Tory colleague's intervention.
Mr Pickles sought to make light of a supposed rift today, describing Mr Paterson as his "brother from a different mother".
Attempting to take the heat out of the spat this afternoon, the Prime Minister said: "I am only interested in one thing, and that is making sure that everything government can do is being done, and will go on being done to help people through this difficult time."
Asked whether Mr Cameron agreed with an unnamed Cabinet minister who was quoted as describing Mr Paterson as "stupid", his spokesman responded: "The Prime Minister's view is that Owen Paterson does an excellent job."
He denied that there had been a lack of urgency in the Government's response during the early stages of the flooding, when the emergency Cobra committee was sometimes chaired by a junior environment minister.
Mr Pickles had been expected to visit the Thames Valley this afternoon, but instead came to the Commons to answer an urgent question on the crisis tabled by Labour.
He flatly denied criticising the "marvellous workforce" at the EA and told the Opposition to stop trying to score "political points".
Mr Pickles was due to chair a Cobra meeting in London this evening, with the Prime Minister participating by phone.
Labour leader Ed Miliband said: "It is a disgrace that you have Government ministers today pointing the finger at each other when they should be rolling their sleeves up and helping those who are affected.
"The Government needs to explain why their response to the flooding has been so slow to help the victims and why their planning has been so inadequate.
The Met Office's Sarah Davies told a briefing that strong winds forecast for the middle of the week could add to the problems facing the country.
Some 20-40mm (0.75-1.5 inches) of rain is expected by Friday night across many southern and western areas.
But some regions, including the already flood-hit south west of England, south Wales, western Scotland and Northern Ireland could have up to 70mm (2.75 inches).
The EA's Pete Fox added: "The very latest figures suggest we have seen around 800 to 900 properties flooded since the end of last week.
"We are still looking and focusing our attention on the Thames. We urge people to look very carefully at the Environment Agency website and make sure they are signed up for free flood warnings.
"You might expect to see some hundreds of properties flooded over the course of the next two or three days."
Network Rail said disruption to lines and infrastructure could take "some months" to resolve.