The cuts would come just as the Government is trying to raise standards in food safety in the wake of the Scottish E.coli crisis.
Chadwick House Group Ltd, the trading arm of the Chartered Institute of Environmental Health, has protested strongly about the effect of the proposals to both David Blunkett, the Education Secretary, and the Further Education Funding Council.
The funding review was outlined in an FEFC consultation paper sent out last November. Recipients were given just a month to respond.
The paper proposed increasing the minimum number of hours of teacher contact from nine to 21 a week, making many college courses no longer eligible for funding. These would include the basic food hygiene and basic health and safety certificates awarded by the Chartered Institute of Environmental Health.
Some 2,000 UK colleges are registered with the institute, authorising them to deliver these qualifications.
The Chartered Institute of Environmental Health fears the changes would force colleges to transfer training from these subjects to others that still qualified for funding.
It would hit all level 1 NVQ courses associated with the food industry and many other NVQ courses that include basic health and safety training.
"It's going to put a lot of responsibility back onto industry to train people if they can't get access to it through colleges," said Dee Waite, training development manager of Chadwick House Group Ltd.
"I've had lots of calls from people saying 'are we going to get the funding next year because if we're not, we're going to have to stop these courses'."
According to the latest figures, food poisoning cases in Britain increased from 63,347 in 1992 to 93,780 last year.
The Pennington report into the Scottish E.coli outbreak recommended that workers handling food should be trained at least to basic food hygiene certificate level.
Simon Williams, spokesperson for the CIEH, said: "Our view is that if the Government is serious about reducing food-borne illness, then it does seem a very strange policy to be making cut-backs in training qualifications."