The proposals, which are subject to parliamentary approval, allow farmers to clear drainage ditches and streams without asking permission.
Farmers had complained that the Environment Agency was micro-managing flood control.
But academics told BBC News that diverting water off farmland could increase floods where people live.
The policy change was announced Environment Minister Liz Truss at the Oxford Farming Conference after what the Department for Environment, Food and Rural Affairs (Defra) said were two successful pilot schemes.
She said: "We will allow farmers across the country to maintain their own ditches up to 1.5km in length from April, so they can clear debris and manage the land."
The decision was welcomed by the National Farmers' Union (NFU).
Its president, Meurig Raymond, said: "The NFU has pressed Defra and the Environment Agency to enable farmers to undertake minor works for many years."
But Professor Alan Jenkins from the Centre for Ecology and Hydrology said he feared the policy could backfire.
"Waterlogged fields are no use to farmers," he said. "They can't maintain their productivity on waterlogged soil so it makes sense for them to manage their fields accordingly.
"There is a potential downside however, in that if we increase drainage in fields during heavy rainfall it's possible there will be increased and faster transmission of water in the river system with a possible increase in flood risk downstream."
Katherine Pygott from the consultancy firm Peter Brett agreed.
"If you are a landowner you may want to maximise productivity on a grouse moor by making it drier - but if you are trying to protect a town you want to keep water back on the uplands.
"It very much depends on local conditions - sometimes it would be unhelpful to speed drainage, sometimes it would not.
"There is a risk of making a free-for-all on drainage. It would be more sensible to make the existing system work."
A government spokesman said over a million acres of prime farmland would be better protected through government investment in flood defences in the 10 years to 2021.
Experts are warning that plans to allow farmers to clear water courses on their land could make floods worse in towns.