The Environment Agency has confirmed that jobs in flood protection in England will be cut as part of a major restructuring of the organisation.
About 1,500 jobs are to be lost at the agency although it is not clear how many flood-related posts will go.
But a spokesman for the agency told the BBC the cuts would have an impact on flood operations such as risk management, maintenance and modelling.
The news comes as large parts of the UK are facing severe flood warnings.
The government says the UK is facing a period of “exceptional weather” in the coming days, due to a combination of high tides, heavy rains and strong winds
There are 188 flood warnings in place across England and Wales, including 14 severe warnings meaning there is a danger to life.
Parts of southern England are only just recovering from widespread flooding before Christmas while coastal areas across the UK suffered heavy flooding following fierce storms in early December.
Asked about the budget cuts, which were first announced in October, spokesman Peter Fox said the Environment Agency, which is responsible for England only, was having to save money and reduce staff numbers along with the rest of the public sector.
But he told BBC News it would seek to “protect front-line responses and flood incident management” and provide the “best services” possible with the reduced resources available.
The Environment Agency, which has an annual budget of £1.2bn, is to reduce staff numbers from 11,250 to about 9,700 by this October.
The BBC’s political correspondent Carole Walker said the cuts would be sensitive given the huge pressure that the organisation is under and the praise it has received from ministers in recent weeks.
Its chief executive Paul Leinster told the environment journal ENDS that it would have an effect on its capacity to support flood defence.
“All of our work on mapping and modelling and new developments in things like flood warning will also have to be resized,” he said.
“And we’re looking at a proportionate reduction in the number of people in flood risk management.”
UKIP leader Nigel Farage said much more needed to be done to prevent flooding and protect homeowners – and called the government “appallingly inept”.
He said: “There are three million homes at risk of flooding in the UK and yet the government is cutting flood defences, allowing thousands of new homes to be built on flood plains, and sitting back and watching the EU block an insurance scheme designed to protect those most vulnerable from losing everything.”
In November 2012, the government announced an extra £120m in funding for flood risk management schemes in response to frequent incidents in previous years.
Ministers insist that long-term capital spending to fund new defences is rising, with total funding on flood defence set to go up from £533m in 2013-4 to £569m in 2014-5.
But critics say funding for maintaining existing defences is set to fall as the Department for the Environment – which oversees the agency – suffers one of the tightest budget squeezes across Whitehall.
A spokesman for the Department for Environment, Food and Rural Affairs (Defra) said: “Departments and agencies across government are having to make choices about their budgets and the Environment Agency is making their own choices about how best to use their resources.”
The BBC’s environment analyst Roger Harrabin said MPs have warned that flooding budgets do not match the risk to communities, especially as climate change was expected to bring more extreme weather.
The Environment Agency issued nearly 7,000 flood alerts and warnings in 2012-13, the largest number in its history.