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Environment Secretary Owen Paterson has complained to Downing Street about Communities Secretary Eric Pickles' criticism of the Environment Agency, the Press Association reports.
Mr Paterson was leading the government response until he was forced to take leave for an eye operation. Mr Pickles is standing in for him on a temporary basis.
Environment Secretary Owen Paterson said the Government is currently spending £100,000 a week on "pumping operations" in the moors and levels in Somerset.
Mr Paterson was responding to an urgent question in the Commons.
Owen Paterson arrived in Somerset last night ahead of an official visit to some of the areas still cut off by flooding later today.
But with locals accusing officials of being slow to act, the visit may prove difficult for the Environment Secretary.
The Environment Secretary Owen Paterson has admitted his department "has had to make efficiencies" after the Environment Agency confirmed that it is making 1,550 redundancies, but said that frontline services will be protected:
Owen Paterson admits his dept (DEFRA) "has had to made efficiencies" and the "intention" of Env Agency boss is to protect frontline services
Owen Paterson: Env Agency chief assures me he will carry those out with the intention of protection frontline services concerned with floods
Paterson: "this govt is spending more on flood defences" <<Capital spend maybe but not flood maintenance budgets - down by £11m
Environment Secretary Owen Paterson has announced he will be chairing a meeting of the Government's Emergency Committee to discuss its response to the flooding expected in many parts of the UK today.
It is thought the meeting will take place early this afternoon.
Mr Paterson said: "The Environment Agency and local authorities have teams on the ground monitoring the situation as it emerges.
"Due to the continuing extreme weather, I will be chairing another Cobra (emergencies committee) meeting today to ensure that everything that can be done to help affected areas is being done.
"With a number of severe flood warnings still in place I urge everyone to follow the advice from the Environment Agency and police and to take every precaution."
Environment Secretary Owen Paterson is expected to chair a meeting of the Government's Cobra emergencies committee tomorrow in response to the flooding which has torn down power lines, closed roads and flooded homes.
The minister said he has been chairing meetings throughout the day to ensure that the Environment Agency and local councils "are on the ground and offering all possible support to their communities".
He is due to chair a Cabinet Office Briefing Room meeting in London tomorrow morning as agencies plan their response to the problem.
Mr Paterson said: "We will remain in touch with local councils in at-risk areas. With a number of flood alerts for the South East for tomorrow, including several areas which have previously been flooded, I urge everyone in affected areas to sign up to EA flood warnings and follow the advice issued."
Environment Secretary Owen Paterson said he had chaired another emergency meeting discussing possible further bad weather after he was accused of disappearing for days as parts of the country were hit by flooding and power cuts.
He said: "With more bad weather forecast for the rest of the week, I have chaired a further emergency COBR meeting to make sure power companies and local authorities are ready to respond quickly. I don't want to see people left without power for days again.
"The Environment Agency will once again be out day and night and I have met their teams in Kent to see for myself how preparations are going. I urge people to sign up for their regular flood warnings and follow their advice."
Shadow environment secretary Maria Eagle criticised Environment Secretary Owen Paterson for "pointing the finger" at energy workers after he accused power companies of letting too many staff go on holiday over the Christmas period.
She said: "As the country faces more severe weather, households that went a week without power and suffered devastating flooding expect to see some action from ministers at long last, not attempts to pass the buck.
"Of course the energy companies must explain why it took so long to get power restored, but Owen Paterson has a nerve pointing the finger at staff being on holiday when he himself has not been seen for days.
"The Environment Secretary has his own questions to answer about his failure to prioritise flood defence investment and deliver the vital flood reinsurance scheme on time, leaving homes without affordable insurance until 2015 and, even then, excluding many properties at risk."