A re-examination of official figures, requested by the Royal Society, has shown that physics and chemistry graduates have declined by two and eight per cent respectively in the last decade.
The news will add to fears in the food industry that a shortage of recruits in the food science sector is set to worsen.
Original figures from the government's Higher Education Statistics Agency said science graduates were up six per cent in the last 10 years.
It also said there were now more than 35 per cent more maths graduates and 12.8 per cent more biology graduates, but a re-analysis has brought these figures down to 7.4 and less than two per cent respectively.
The government had masked true figures by counting students on combined degree courses in with those on single subject degrees, the Royal Society said.
Professor Judith Howard, chair of the Royal Society's Higher Education working group, said: "At a time when there are concerns over whether the education system can provide enough scientifically skilled people for the UK to be a globally competitive economy, it is extremely important that we have a sound picture, based on consistent data, of what is happening in our universities."
Most of the increase in science graduates has been attributed to psychology, sports science and computer science, instead of core subjects.
The Royal Society warning comes in stark contrast to comments from British prime minister Tony Blair, who has frequently described the UK as a strongly emerging 'knowledge-based' economy.
The food industry already faces an acute shortage of food science recruits for its research and development activities. Most of these recruits traditionally come from core science subjects and maths.
Applicants for food science degree courses have more than halved in the last decade, while Britain's Institute of Food Science and Technology has warned the sector is struggling to fill empty seats.
Some in the industry believe the UK's food research capability is now in serious danger. "I'm not sure there really is a UK research base anymore," said Donald Muir, a senior ex-research head told this website.
Muir's old research centre, the Hannah Institute in Scotland, closed down in spring this year to the concern of both unions and scientists. The centre had been responsible for world-class dairy research, including extending the shelf life of milk and analysis of microbacteria and caseins in dairy products.
Muir said he feared the closure could put the UK dairy industry at a competitive disadvantage. "It was the final nail in the coffin. Some of the bigger companies still have substantial R&D facilities, but these tend to be multinational firms with headquarters outside the UK."