The firm said that toddler nutrition is largely neglected when it comes to public health polices and programs run by Mend could help address the imbalance.
Nutricia is supporting a trial program designed to help educate parents about the best way to feed their child.
If successful the group say the trial could be rolled out on national agendas.
But the arrangement has been branded as " completely inappropriate" by the campaign group Baby Milk Action.
Policy director Patti Rundall said: "This is the sort of thing I cannot bear.
It is a completely inappropriate to have a conflict of interests."
Rundall added that nutrition companies should stay away from any involvement in providing information to parents about how to feed their child.
Nutricia denied this was a marketing attempt.
A spokesperson told NutraIngredients.com: " I would refute the argument that this is an attempt to merchandise Nutricia products.
"This initiative is about better outcomes for today's toddlers, in an attempt to prevent them becoming obese adults.
Nutricia wants to share their knowledge and expertise.
They recognise that they need to work in partnership with a variety of stakeholders, to be part of the solution to the obesity epidemic."
The agreement will see Nutricia provide money to Mend to carry out the trial program.
Market value Infant nutrition is big business.
According to analysts at Euromonitor, the milk formula market in Europe is worth the most in France, which this year is recorded at €597m, with Spain at €296m and the UK at €267m. Increasingly companies have been looking for the best way of replicating the healthy profile of breast milk.
Nutricia is part of Royal Numico, which reported €523m baby food sales this third quarter.
Mend is a social enterprise organisation established in 2004 to run programmes aimed at reducing the problem of childhood overweight and obesity levels.
They will be working on a new programme which will run for 10 weeks and is aimed at encouraging parents and toddlers to taste new foods.
Parents also discuss food types and portion sizes, learn how to read food labels, and find out ways to deal with fussy eating.
A field trial of this programme is currently taking place at five sites in Lewisham, Hillingdon, South Tyneside and Plymouth, and is supported by a " donation " from Nutricia.
A spokesperson said the agreement did not involve supplying food products.
The exact amount of money could not be revealed, but the spokesperson added it was a "significant amount."
Dr Tahsin Yasin, medical director at Nutricia UK, said that toddler nutrition is a much-neglected area of public health policy, with the majority of literature and policy frameworks referring to school age children, adolescents and adults.
Dr Yasin said, "It's a common mistake that it's acceptable to feed toddlers the same diet as adults but in smaller portions.
We believe that addressing nutritional needs at this age may actually hold the key to healthier children and adults and in the long term benefit both individuals and the economy as a whole.
"Our hope is that through the evidence generated through the field trial and other clinical studies, we can help establish a national programme for under-5s in partnership with government, local authorities and other interested stakeholders."
Infant obesity Statistics from the Department of Health show a 10 percent rate of obesity in girls and 12 percent in boys aged 2 to 5 years.
The Department's forecast for 2010 predicts a dramatic rise to 23 percent of girls and 25 percent of boys overweight or obese.
The Foresight Report on obesity in the UK estimated that the total cost of the problem could reach £45bn (€63m).
Moreover, better nutritional advice in a child's early years can help in disease prevention, iron deficiency, anaemia and rickets are two of the fastest growing diseases in toddlers and infants in the UK.
Paul Sacher, from Mend, added: "Proper nutrition during the early years is paramount for children to grow up healthy, and bad habits begin young."
Infant nutrition has come to the forefront in government policy as far labelling of products are concerned.
New regulations have been proposed by the European Commission to cover a broad range of points hinged around making sure the nutritional value for any formula satisfies the nutritional requirements of the infant.
But the subject has caused controversy as pressure groups say advertisements for formula are putting mothers off breastfeeding, and have called for a complete ban.