The Ministry of Agriculture, Fisheries and Food has promoted school kitchens to the status of "catering outlets", ranking them with corner cafes and multi-national burger chains.
School tuck shops are also under threat - with warnings of a possible pound;90 charge for selling snacks, biscuits and drinks.
Even where the lunchtime meals are cooked elsewhere and only served on the premises, schools must pay the pound;600.
The issue has upset Nigel de Gruchy, leader of the second biggest teacher union. the National Association of Schoolmasters Union of Women Teachers. He has written to both Education Secretary David Blunkett and agriculture minister Jeff Rooker warning about the effect on education budgets.
The levy will have a disproportionate impact on different schools, he argues, with pound;600 equalling the year's budget for books and equipment in a small primary or a secondary school subject department.
The total bill in a large metropolitan education authority could add up to around pound;250,000, he adds.
"We have no doubt that if the Government were to pursue such a policy, it would be viewed as unjust and unnecessary by those involved in education and by the public," writes Mr de Gruchy in his letter to MAFF.
"While education ministers are apparently striving to obtain extra funding for schools, if this charge is imposed a significant proportion of the money obtained will be returned to another government department."
A spokeswoman for MAFF said: "We are intending that it will apply to schools, but we are still consulting."