Nutritionists recommend girls during puberty drink at least a glass of milk a day, preferably with their lunch, to stave off brittle bone disease in later life. The best time to encourage this is during their primary years.
John Duncan, chief executive of Scottish Milk, said that a European Union scheme to withdraw the subsidy next July could increase the cost of milk to schools by a third.
The subsidy for secondary schools was removed three years ago, leading to a "significant drop" in milk consumption.
Dr Judy Buttriss, science director at the British Nutrition Foundation, said: "Milk provides such a wide range of nutrients it's almost like the original fast food. It has got lots of important things for growth."