Across-the-board cuts in research at the Department for Environment, Food and Rural Affairs have been condemned by science campaigners.
The first joint research budget for the merged Ministry of Agriculture, Fisheries and Food and the Department of the Environment, Transport and Regions has been set at about 3 per cent lower than last year.
Defra's research remit includes animal health and welfare, genetically modified organisms, agriculture and environmental protection. Many of its responsibilities were inherited from Maff, which had been criticised in scientific circles for years of cuts.
Peter Cotgreave, director of the pressure group Save British Science, said a healthy research programme was vital in order to respond rapidly to crises such as foot-and-mouth disease or concern about GM crops.
"Maff's research and development spending has gone down in real terms every year since 1986 with one tiny blip. For Defra to cut it again is thoroughly irresponsible," he said.
Dr Cotgreave said that while the Office of Science and Technology was fighting hard to raise science spending, other departments, such as Defra, were not taking it seriously.
Nevertheless, Defra recently appointed a chief scientific adviser and started a review of its institutions.
A spokesman said: "No live projects have been stopped through lack of funding. Some projects will begin later than originally planned in agreement with contractors."
The spokesman added that additional bids for science had been made to the forthcoming comprehensive spending review.
But an insider familiar with Defra's funding described the budget reduction as death by a thousand cuts. "People are worn out by it," he said. "They have to fight harder and harder just to maintain the same level of funding." He said the problem was due partly to difficulties involved in the departmental merger.
In 2000, the House of Commons science and technology committee published a report on governmental research spending that projected Maff would have lost 32 per cent of its scientific expenditure between 1986 and 2002.
The weight of the cuts had fallen on areas such as arable crop research, plant health and animal disease control. The Biotechnology and Biological Sciences Research Council is negotiating with Defra over the future of jointly funded research establishments.