The Environment Agency (EA) is not planning cuts to front- line flood defence services, Owen Paterson has said.
Speaking after a meeting of Government emergency committee Cobra, the Environment Secretary rejected claims flood defences were being cut.
Mr Paterson said: "Like all departments, this department has had to make efficiencies given the dire financial position we inherited when we came to office.
"I had a meeting this morning with the chief executive of the Environment Agency.
"He has assured me he has every intention of protecting front-line services concerned with flooding.
"His intention is to protect front-line services as he makes his efficiencies.
"This Government is spending more than any previous government on flood defences - 165,000 properties will be protected by 2015."
The Cobra meeting included representatives from across Government, including the Department of Communities and Local Government (DCLG), the Home Office and the Department for Energy and Climate Change (DECC).
The meeting, chaired by Mr Paterson, was told 3,500km of coastal flood defences were tested by the overnight storms and 130,000 homes were protected.
As the latest bout of extreme weather batters the country, the EA's chief executive, Paul Leinster, warned that Government cuts will "impact" how the organisation deals with flooding.
About 550 staff from the floods team are facing job losses, according to environmental policy magazine The ENDS Report.
Mr Leinster told the magazine: "Flood risk maintenance will be [further] impacted. All of our work on mapping and modelling and new developments in things like flood warning will also have to be resized. And we're looking at a proportionate reduction in the number of people in flood risk management."
Trade unions warned the cuts to staff would inevitably impact on services.
Unison national officer for the Environment Agency Matthew Lay said: " Staff in the agency have worked day and night to keep communities safe and prevent flood damage, and work tirelessly to support those devastated by the aftermath.
"The Government can't have it both ways, praising the sterling work of members in the agency but at the same time imposing further damaging cuts."
GMB national officer Justin Bowden said: "The public need to know that job losses on this scale will impact specifically directly on flood risk management, on flood defence operations teams managing flood defences and carrying out river maintenance to enable flows to be conveyed away, enhancing the river's ecology and supporting fish stocks.
"These teams also provide wider incident response containing river pollution, aerating watercourses to prevent fish deaths from low oxygen levels. So cutting flood risk funds will have a detrimental affect on the health of all rivers no matter what the interest."
The flood risk appeared to be receding this afternoon as the latest storm moved away from Britain.
Just after 2.30pm, eight severe flood warnings were still in force, down from a peak of more than 20 overnight. More than 300 other flood warnings were also in force ahead of another expected very high tide this evening.
Last night, homes in Newport, South Wales, were evacuated because of the risk of flooding as Wales prepared for the highest tides in 17 years. Residents at the Lighthouse Park Estate were taken to a nearby leisure centre as a precaution, and coastguards have been warned of a storm bringing 70mph winds.
People living in Ilfracombe, Devon, were joined by emergency services during the night as they gathered sand from beaches to build flood defences.
The storms have already claimed at least two lives. The body of a 27-year-old man from Surrey was found on Porthleven Sands beach in Cornwall. He had been swept out to sea on New Year's Eve night, having gone for a paddle with friends at nearby Loe Bar.
In a second tragedy on Tuesday, a woman died after being swept out to sea at the popular beauty spot Croyde Bay in north Devon. The woman, who was believed to be on holiday with her family, was rescued from the sea and airlifted to hospital before being confirmed dead by doctors.
Elsewhere, in Dorset a search was carried out for a man who is believed to have fallen into the River Stour, near Iford Bridge in Christchurch.
In Scotland heavy rain and gusts of up to 60mph could sweep across the country today, bringing further disruption after days of wet weather.
High tides and a storm surge have increased the risk of flooding in the Firth of Clyde, according to the Scottish Environment Protection Agency (Sepa).
Last night residents of Sydenham in east Belfast were told to pack a bag and prepare for potential evacuation. Sandbags were distributed to the public through the night while the authorities built up river defences.
But this morning the Police Service of Northern Ireland (PSNI) said more positive meteorological reports, combined with the defence work undertaken, suggested the densely packed neighbourhood may avoid "serious flooding".