But in 2009, the FSA warned that children were now consuming so much fat that it was clogging their arteries. Parents are now advised to switch their children to semi-skimmed milk from the age of two.
The new research suggests such efforts could be counter-productive.
Children who drank full-fat milk were likely to end up less hungry, researchers suggested, making them less likely to snack on high calorie foods.
The Canadian research, published in the American Journal of Clinical Nutrition, found that those children who drank whole milk had a Body Mass Index score that was 0.72 units lower than those who drank one or two per cent semi-skimmed milk.
Lead researcher Dr Jonathon Maguire, a paediatrician at St Michael's Hospital in Toronto, said the difference amounted to the difference between having a healthy weight and being overweight.
Children who drank one cup of whole milk each day had comparable vitamin D levels to those drinking nearly three times as much skimmed milk, the study found.
This could be because vitamin D is fat soluble, meaning it dissolves in fat rather than water.
Prof Maguire said: "Children who drink lower fat milk don't have less body fat, and they also don't benefit from the higher vitamin D levels in whole milk. It's a double negative with low fat milk."