Parents had made complaints on the brand's Aptaclub UK Facebook page after recent changes to the formulas of three of its milks. Danone UK said that extensive quality and safety checks had been made but added that it is taking "all feedback very seriously".
"We are very concerned to hear reports of babies being unsettled or unwell and we will investigate every complaint," it said in a statement.
"We would like to reassure parents that the quality and safety of our products is our number one priority."
Mixing instructions on Aptamil packs have been updated, the company said, because the new formula requires parents "to mix it up slightly differently compared with the previous formulation -specifically, shaking vigorously for 10 seconds to dissolve the powder".
While the company investigates the complaints it has set up a free helpline for parents to call for advice.
Danone shares lost 2 percent on Monday on the Paris bourse.
The group's sales have been boosted in recent quarters by the strong performance of its baby food division, thanks notably to strong demand for its Aptamil and Nutrilon brands in China, where consumers are highly sensitive after melamine-tainted baby milk led to the deaths of six children in 2008.
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