Subject to further follow-up, the findings add weight to the idea that a tendency towards obesity is set in earliest childhood.
They come shortly after another study indicated that tendency towards obesity could be genetic.
Professor Berthold Koletzko, project co-ordinator from the University of Munich, Germany, said the results "emphasise the importance of promotion of and support for breastfeeding, together with the development of the right composition of infant formula, and support for the choice of appropriate complementary food."
The study involved 990 infants and ran from October 2002 to July 2006, when the youngest participants reached the age of two.
The researchers hypothesised the primary hypothesis that one possible causal factor for the difference in long-term obesity risk between breast and formula-fed infants is the much lower protein content of breast milk compared to infant formula.
The infants were randomised to receive either a low-protein formula (1.8g/100kcal, then 2.25g/100kg in follow on formulas) or a high protein formula (3g/100kcal, then 4.5g/100kcal).
The intervention lasted for 12 months from birth, and the infants were followed until they reached the age of two.
A group of breast-fed children was also followed.
In addition to a body growth rate similar to that of breast-fed babies, those in the low protein group were seen to have metabolic and endocrinal benefits too.
It is emphasised that the low protein content in the formula is considered safe and is in accordance with the formula composition authorised by the EU.
No untoward effects were seen during the study.
The programme is part of the Early Nutrition Programming Project (EARNEST), an EU-funded project to investigate the link between nutrition in earliest childhood and health outcomes later in life.
The results are being presented today at the pre-congress EARNEST satellite conference of the 15 th European Congress on Obesity in Budapest by Prof Koletzko.
A spokesperson told NutraIngredients.com it is expected that the study will be published, but it is not yet known when and in which journal.
The full results have not been seen by NutraIngredients.com.
However these results are not the end of the story.
"These first results of the EU Childhood Obesity Programme contribute to the growing body of scientific evidence that early nutrition can exert important long term 'programming' effects on early development and later health," said Prof Koletzko.
Further follow up of the children is planned under the aegis of EARNEST, to investigate whether the observed effects at age two are associated with a lower risk of obesity at a later age.