The Food Standards Agency's (FSA) profiling proposal, developed at the end of July, used zero as a benchmark, with positive scores indicating unhealthy products and minus scores pointing to healthier options.
Dairy UK said it had serious concerns about the FSA's plans, which say whole, semi-skimmed and flavoured milk have the same health value as diet fizzy drinks. All got a score of zero.
Channel Island whole milk was marked as a 2, making it as unhealthy as ordinary fizzy coke drinks.
"We question the omission of micronutrients such as protein quality, minerals such as calcium, phosphorus, potassium and magnesium, as well as vitamins A and B," said Ed Komorowski, Dairy UK's technical director, as part of an FSA consultation period that ended this week.
The health benefits of milk have been subject to much debate recently, particularly the potential connection between dairy and weight loss. The calcium content of milk, however, is widely accepted as good for womens' bones - helping to protect against osteoporosis.
Dairy UK also criticised the FSA model of judging foods per 100g instead of per serving to reflect pack sizes in supermarkets.
Others have also criticised this policy. A report from the National Consumer Council said that one of the authors involved in the nutrition proposals "expressed his disappointment that there was insufficient time to discuss the basis of the model (per 100g, per 100kJ or per serving), and told the participants that this would need to be explored in more depth to move the model forward".
The FSA said at the end of July that it was confident in the accuracy of its profiling. Points are allocated on the basis of the level of each nutrient (or food component) in 100g of the food, including the energy, saturated fat, total sugar, and sodium content of the food, as well as the amount of protein, fibre and fruit and vegetables that it contains.
Yet, one other slightly puzzling result was the FSA's assertion that olive oil was less healthy than a range of potato crisps, chocolate biscuits and cakes.
Olive oil received a score of 20, despite a number of studies showing that a so-called Mediterranean diet, with a high ratio of monounsaturated fatty acids (mostly olive oil) to polyunsaturated fatty acids, has a protective effect on the heart.
Dairy UK's Komorowski said the current profiling scheme meant that breast milk would fall into the category 'high in saturated fat, salt or sugar'.
"We question the scientific basis of a model which results in breast milk being classified as unsuitable for children," he said, adding that the positioning of cheese as similarly unsuitable raised "serious doubts".
The FSA is proposing that the definition of high in saturated fat, salt or sugar should apply to foods scoring four points or more, and drinks scoring one point or more.
The profiling is intended to be more straightforward for food companies, enforcement bodies and regulators to use than earlier models as it is based on the information already included in on-pack nutritional labelling.