Otago University food scientist Pat Silcock said ingredients in infant formula were tightly controlled because they were the sole source of nutrients for bottle-fed babies.
"There needs to be good data to justify the addition of an ingredient," Mr Silcock said.
FOS reportedly functioned as a "prebiotic" - aiding gut bacteria and softening babies' poo, he said.
"The idea of adding it is to try to compensate for the lack of prebiotics in infant formula."
FOS was put in a range of baby formula in 2007 without permission, prompting Food Standards to advise parents to switch brands.
In 2009, FOS was specifically excluded when a similar compound, inulin, was permitted by the agency.
But it has since appeared in formula anyway as a derivative of inulin, Food Standards says. Allowing FOS to now be manufactured by a proposed process - using an enzyme made by a fungus - will be "as safe".
The authority is seeking submissions on the proposal.
Women's Health Action Maternal and Child Health promoter Isis McKay said the consultation process was to be applauded.
But Food Standards needed to carefully consider the risks and benefits of an additional ingredient, she said.
"The composition of breastmilk is uniquely suited for each individual baby and cannot be replicated by the addition of a fungally-derived sugar-like substance," Ms McKay said.
Food Standards' proposal to allow FOS was sparked by an application from manufacturer GTC Nutrition.
The firm provided several studies showing the safety and benefits of FOS. Food Standards says the studies show FOS has potential benefits and is unlikely to cause adverse physiological effects.
Ingredient types
Oligosaccharides: Short chains of sugar (carbohydrates).
Human milk oligosaccharides: Hundreds of different oligosaccharides are found in breast milk, helping nurture gut bacteria and digestion.
Fructo-oligosaccharides: Because cows' milk formula has few oligosaccharides, manufacturers hope adding fructo-oligosaccharides will help bottle-fed babies digest as well as they would on human milk.
Inulin: A natural carbohydrate whose chain is generally longer than what is normally called a fructo-oligosaccharide, but otherwise similar. Already allowed in infant formula.
Prebiotics: Foods that cannot be digested by people and instead stimulate the growth of beneficial bacteria in the gut.