Gwyn Jones, head of the dairy board at the National Farmers' Union, said he was "disappointed that whole milk has been bracketed with a range of junk foods".
He also requested a meeting with education authorities to amid concerns over the future of dairy products in schools after 2008.
Whole milk is set to be banned from England's schools from this autumn alongside 'junk foods' like fizzy drinks, crisps and confectionery, as part of a government push to make children eat more healthily.
Jones, who wrote a letter to education authorities criticising the move, said whole milk was naturally full of nutrients and only contained 3.5 per cent fat.
The dairy industry's concern is not directly about revenues, which are fairly negligible in schools, but more about what the government strategy says to consumers already confused about the health benefits of dairy products.
Various debates on this have been played out in the national media recently, with some citing studies that questioned the need for dairy in the diet.
The dairy industry, inevitably, sees government support as crucial in winning over the public, which has led to various spats between the two recently.
Industry body Dairy UK lashed out last autumn at the Food Standards Agency's (FSA) nutrient profiling proposals, which said whole, semi-skimmed and flavoured milk have the same health value as diet fizzy drinks.
It criticised the FSA for ignoring micronutrients in foods, such as calcium and magnesium.
Despite the FSA proposals, the government has since offered support by promising to continue subsidising milk in infant schools and stating it wanted the only drinks available in secondary schools to be milk, juice and water.
It has hinted for several months that these policies did not extend to whole milk, however.
Jim Knight, then under-secretary of state for the Department of Environment, Food and Rural Affairs, told Parliament earlier this year that skimmed or semi-skimmed milk was "recognised as a valuable component of a balanced diet and a healthier alternative to soft drinks".
In reality, whole milk has been on the wane in Britain for some time, largely due to consumer concerns over fat in their diets.
Whole milk consumption per person per week fell by nearly 75 per cent between 1985 and 2004, according to figures from the Milk Development Council. People now drink twice as much semi-skimmed milk, around one litre per week, as whole milk.
Milk consumption generally had been falling for around 40 years in Britain, until added value brands from the big dairy processors halted the slide last year.